import scipy.io as sio
import pandas
from pandas import Series,DataFrame,Panel
from trnlib.data_utility import *
from trnlib.model_utility import *
from trnlib.MOMA_and_t_p_FBA import *
from trnlib import settings
from trnlib import visual
from cobra.manipulation import modify
from IPython.core.display import HTML
from IPython.display import SVG
from matplotlib.pyplot import *
pycobra_model = load_model('/annotation/iJO1366.pickle')
modify.convert_to_irreversible(pycobra_model)
sampled_anaerobic_101 = sio.loadmat(settings.dropbox_trn_directory+'/analysis/sampling/sampling_results/sampled_pFBA_anaerobic_model_101.mat')['sampled_pFBA_anaerobic_model_101']
sampled_nitrate_101 = sio.loadmat(settings.dropbox_trn_directory+'/analysis/sampling/sampling_results/sampled_pFBA_nitrate_model_101.mat')['sampled_pFBA_nitrate_model_101']
anaerobic = ome.query(Condition).filter_by(eacceptor='anaerobic').one()
nitrate = ome.query(Condition).filter_by(eacceptor='NO3').one()
def get_sampling_dict(sampled_model, pycobra_model):
sampling_dict = {}
reject_dict = {}
for i,rxn_name in enumerate(sampled_model[0][0][1]):
#translate matcobra rxn ID strings to cobrapy rxn ID strings
rxn_name = str.replace(str(rxn_name[0][0]),'(','_').replace(')','').replace('-','__')
if rxn_name[-2:] == '_f': rxn_name = rxn_name[:-2]
elif rxn_name[-2:] == '_b': rxn_name = rxn_name[:-2] + '_reverse'
#if it can't be translated then store it in an accessory dict for debugging
try:
pycobra_model.reactions.get_by_id(rxn_name)
sampling_dict[rxn_name] = sampled_model[0][0][20][i]
except: reject_dict[rxn_name] = sampled_model[0][0][20][i]
sampling_dict['total_flux'] = sampled_model[0][0][8][-1][0]
return sampling_dict,reject_dict
def find_used_rxns(metabolite, sampling_dict, pycobra_model, cutoff):
met_rxns = list(metabolite._reaction)
used_met_rxns = {}
for rxn in met_rxns:
if rxn.id == 'Ec_biomass_iJO1366_core_53p95M': continue
if abs(mean(sampling_dict[rxn.id])) >= cutoff:
#used_met_rxns[rxn] = [mean(sampling_dict[rxn.id]), std(sampling_dict[rxn.id])]
used_met_rxns[rxn] = mean(sampling_dict[rxn.id])
return used_met_rxns
def make_reactions_DataFrame(metabolite, rxn_dict, condition, total_flux):
index = [[],[],[],[]]
data = [[],[],[],[],[],[]]
for rxn in rxn_dict:
if len(rxn._genes.keys()) < 1 or rxn._genes.keys() == ['s0001']: continue
flux = rxn_dict[rxn]
coefficient = rxn._metabolites[metabolite]
if coefficient*flux > 0:
index[0].append('producing')
else: index[0].append('consuming')
regulation_frame = get_regulation_frame(rxn, ['ArcA','Fnr'], condition)
index[1].append(rxn.id)
index[2].append(regulation_frame.any()['value'])
index[3].append(regulation_frame.any()['novel'])
data[0].append(flux)
data[1].append(flux/total_flux)
data[2].append(str([ome.query(Gene.name).filter_by(bnum=gene.id).scalar() for gene in rxn._genes.keys()]))
data[3].append(float(regulation_frame['novel'].count()))
data[4].append(float(regulation_frame['value'].count()))
data[5].append(regulation_frame['value'].sum())
return DataFrame(array(data).T, index, columns=['flux','percent_total','genes','novel_regulation','total_regulation', 'direction'])
def make_metabolite_panel(metabolites, sampling_dict, model, condition):
met_dict = {}
for metabolite in metabolites:
used_rxns = find_used_rxns(metabolite, sampling_dict, pycobra_model, cutoff=1e-4)
rxn_df = make_reactions_DataFrame(metabolite, used_rxns, condition, sampling_dict['total_flux'])
met_dict[metabolite.id] = rxn_df
return Panel(met_dict)
electron_donors = ['pyr_c', 'lac__D_c', 'for_c', 'h_c', 'h_p', 'h_e','h2_c', 'h2_p', 'ac_c', 'glyc3p_c', 'etoh_c', 'mal__L_c', 'fum_c', 'succ_c']
electron_carriers = ['nadh_c', 'nadph_c','fadh2_c', 'gthrd_p', 'gthrd_e', 'gthrd_c', 'amet_c']
biomass_precursors = ['g6p_c','f6p_c','g3p_c','13dpg_c','3pg_c','pep_c','pyr_c','e4p_c','r5p_c','accoa_c','oaa_c','succoa_c','akg_c']
all_mets = [pycobra_model.metabolites.get_by_id(met_id) for met_id in electron_donors+electron_carriers+biomass_precursors]
sampled_anaerobic_dict_101, sampled_anaerobic_dict_101_reject = get_sampling_dict(sampled_anaerobic_101, pycobra_model)
sampled_nitrate_dict_101, sampled_nitrate_dict_101_reject = get_sampling_dict(sampled_nitrate_101, pycobra_model)
anaerobic = ome.query(Condition).filter_by(eacceptor='anaerobic').one()
nitrate = ome.query(Condition).filter_by(eacceptor='NO3').one()
metabolite_panel_anaerobic_101 = make_metabolite_panel(all_mets,sampled_anaerobic_dict_101, pycobra_model, anaerobic)
metabolite_panel_nitrate_101 = make_metabolite_panel(all_mets,sampled_nitrate_dict_101, pycobra_model, nitrate)
nice_names = {'pyr_c':'Pyr', 'lac__D_c':'Lac', 'for_c':'For', 'h_c':'H_c', 'h_p':'H_p', 'h_e':'H_e', 'h2_c':'H2', 'h2_p':'H2', 'ac_c':'Ac',\
'etoh_c':'Eth', 'mal__L_c':'Mal', 'fum_c':'Fum', 'succ_c':'Suc', 'nadh_c':'NADH', 'nadph_c':'NADPH',\
'fadh2_c':'FADH', 'gthrd_p':'GTH_p', 'gthrd_e':'GTH_e', 'gthrd_c':'GTH_c', 'amet_c':'AMET', 'g6p_c':'G6P',\
'f6p_c':'F6P', 'g3p_c':'G3P', '13dpg_c':'BPG', '3pg_c':'3PG', 'pep_c':'PEP', 'pyr_c':'PYR', 'e4p_c':'E4P',\
'r5p_c':'R5P', 'accoa_c':'AcoA', 'oaa_c':'OAA', 'succoa_c':'ScoA', 'akg_c':'AKG','glyc3p_c':'GLYC3P'}
def draw_node_map_table(metabolite_panels, labels, molecules):
table = '<table border="1">'
table += '<tr><th>'+labels[0]+'</th><th>'+labels[1]+'</th></tr>'
for molecule in molecules:
table += '<tr>'
for panel in metabolite_panels:
table += '<td>'
str(visual.MetaboliteNodeMap(panel[molecule],nice_names[molecule]))
table += str(visual.MetaboliteNodeMap(panel[molecule],nice_names[molecule]))
table += '</td>'
table += '</tr>'
table += '</table>'
return HTML(table)
draw_node_map_table([metabolite_panel_anaerobic_101, metabolite_panel_nitrate_101], ['Fermentation', 'Nitrate Respiration'], electron_carriers+electron_donors)
Fermentation | Nitrate Respiration |
---|---|
draw_node_map_table([metabolite_panel_anaerobic_101, metabolite_panel_nitrate_101], ['Fermentation', 'Nitrate Respiration'], biomass_precursors)
Fermentation | Nitrate Respiration |
---|---|
df = metabolite_panel_anaerobic_101['h_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(columns=['flux']).sort(ascending=True).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
consuming | 3OAR140 | False | False | 0.0110742045993 | 2.73644725178e-05 | [u'fabG'] | 0.0 | 0.0 | nan |
ACALD_reverse | True | False | 8.08683403253 | 0.0199826493772 | [u'adhE', u'mhpF'] | 0.0 | 1.0 | 0.587546853664 | |
ACHBS | False | False | 0.0683735554976 | 0.00016895175302 | [u'ilvB', u'ilvH', u'ilvN', u'ilvI'] | 0.0 | 0.0 | nan | |
ACLS | False | False | 0.205755221604 | 0.000508423251214 | [u'ilvB', u'ilvH', u'ilvN', u'ilvI'] | 0.0 | 0.0 | nan | |
AGPR_reverse | False | False | 0.0814776053093 | 0.000201331993762 | [u'argC'] | 0.0 | 0.0 | nan | |
ALCD2x_reverse | True | False | 8.0873620921 | 0.0199839542178 | [u'adhP', u'adhE', u'frmA'] | 0.0 | 1.0 | 0.587546853664 | |
ASAD_reverse | False | False | 0.255916923253 | 0.00063237332762 | [u'asd'] | 0.0 | 0.0 | nan | |
ATPS4rpp_reverse | False | False | 6.44426711942 | 0.0159238497813 | [u'atpF', u'atpE', u'atpC', u'atpD', u'atpG', u'atpB', u'atpI', u'atpH', u'atpA'] | 0.0 | 0.0 | nan | |
DAPDC | False | False | 0.0807599744013 | 0.000199558720469 | [u'lysA'] | 0.0 | 0.0 | nan | |
DASYN160 | False | False | 0.0146894664461 | 3.62978214156e-05 | [u'cdsA'] | 0.0 | 0.0 | nan | |
DASYN161 | False | False | 0.0114253827658 | 2.82322373491e-05 | [u'cdsA'] | 0.0 | 0.0 | nan | |
DHDPRy | False | False | 0.0874390302466 | 0.000216062735586 | [u'dapB'] | 0.0 | 0.0 | nan | |
DHORTS_reverse | False | False | 0.0804388562323 | 0.000198765234198 | [u'pyrC'] | 0.0 | 0.0 | nan | |
FADRx | False | False | 0.486584852294 | 0.00120235613301 | [u'fre'] | 0.0 | 0.0 | nan | |
G3PD2_reverse | False | False | 0.0414638909066 | 0.000102457697347 | [u'gpsA'] | 0.0 | 0.0 | nan | |
G5SD | False | False | 0.0520233469134 | 0.000128550220843 | [u'proA'] | 0.0 | 0.0 | nan | |
GLGC | False | False | 0.0406105903609 | 0.000100349182995 | [u'glgC'] | 0.0 | 0.0 | nan | |
GLUDy_reverse | False | False | 2.01170910993 | 0.00497095372935 | [u'gdhA'] | 0.0 | 0.0 | nan | |
HACD1 | True | False | 0.0777672212243 | 0.000192163596843 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD2 | True | False | 0.0797551048851 | 0.000197075677645 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD3 | True | False | 0.078168917303 | 0.000193156191951 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD4 | True | False | 0.0785905927577 | 0.0001941981563 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD5 | True | False | 0.0780245278058 | 0.000192799404031 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD6 | True | False | 0.0679896617665 | 0.000168003147695 | [u'fadJ', u'fadB'] | 0.0 | 2.0 | -6.44117175826 | |
HACD7 | True | False | 0.0673410991948 | 0.000166400542966 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD8 | True | False | 0.0143419864279 | 3.54391947465e-05 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HSDy_reverse | False | False | 0.167898854474 | 0.000414879781914 | [u'thrA', u'metL'] | 0.0 | 0.0 | nan | |
IGPS | False | False | 0.0133774874225 | 3.30559078666e-05 | [u'trpC'] | 0.0 | 0.0 | nan | |
KARA1_reverse | False | False | 0.208950714224 | 0.000516319346071 | [u'ilvC'] | 0.0 | 0.0 | nan | |
KARA2 | False | False | 0.070918719906 | 0.000175240880234 | [u'ilvC'] | 0.0 | 0.0 | nan | |
MTHFR2 | False | False | 0.0382350940411 | 9.44793073599e-05 | [u'metF'] | 0.0 | 0.0 | nan | |
OMPDC | False | False | 0.0775813861268 | 0.000191704396422 | [u'pyrF'] | 0.0 | 0.0 | nan | |
P5CR | False | False | 0.0520233469143 | 0.000128550220845 | [u'proC'] | 0.0 | 0.0 | nan | |
PPNDH | False | False | 0.0436004754919 | 0.00010773721965 | [u'pheA'] | 0.0 | 0.0 | nan | |
PSD160 | False | False | 0.0106963709769 | 2.6430841783e-05 | [u'psd'] | 0.0 | 0.0 | nan | |
PYK | True | True | 0.0975618664448 | 0.000241076367081 | [u'pykF', u'pykA'] | 1.0 | 1.0 | 3.6770040631 | |
SHK3Dr | False | False | 0.092275546831 | 0.000228013817397 | [u'aroE', u'ydiB'] | 0.0 | 0.0 | nan | |
SULRi | False | False | 0.0600301245591 | 0.000148335050072 | [u'cysI', u'cysJ'] | 0.0 | 0.0 | nan | |
TRDR | False | False | 0.055196218587 | 0.00013639041911 | [u'trxA', u'trxC', u'trxB'] | 0.0 | 0.0 | nan | |
UAGDP | False | False | 0.0173064007941 | 4.27642928815e-05 | [u'glmU'] | 0.0 | 0.0 | nan | |
producing | ACGS | False | False | 0.0793034040047 | 0.000195959520162 | [u'argA'] | 0.0 | 0.0 | nan |
ADSK | False | False | 0.0600301245594 | 0.000148335050072 | [u'cysC'] | 0.0 | 0.0 | nan | |
ADSS | True | True | 0.070324691367 | 0.000173773029655 | [u'purA'] | 1.0 | 1.0 | 1.07983758257 | |
AIRC2 | False | False | 0.105322101164 | 0.000260251986225 | [u'purK'] | 0.0 | 0.0 | nan | |
ANS | False | False | 0.0133774874225 | 3.30559078666e-05 | [u'trpE', u'trpD'] | 0.0 | 0.0 | nan | |
ARGSS | False | False | 0.0696121489569 | 0.000172012330092 | [u'argG'] | 0.0 | 0.0 | nan | |
ASNS2 | False | False | 0.0567301957889 | 0.000140180892422 | [u'asnA'] | 0.0 | 0.0 | nan | |
ASPCT | False | False | 0.0775813861268 | 0.000191704396422 | [u'pyrB', u'pyrI'] | 0.0 | 0.0 | nan | |
CBMKr | False | False | 0.151804559264 | 0.000375110614294 | [u'yqeA', u'yahI', u'ybcF'] | 0.0 | 0.0 | nan | |
CS | True | False | 0.263545269736 | 0.000651223049586 | [u'gltA'] | 0.0 | 1.0 | -3.39561619493 | |
CTPS2 | False | False | 0.0376417123582 | 9.30130551692e-05 | [u'pyrG'] | 0.0 | 0.0 | nan | |
CYSS | False | False | 0.0600301245583 | 0.00014833505007 | [u'cysK', u'cysM'] | 0.0 | 0.0 | nan | |
DHDPS | False | False | 0.0874390302466 | 0.000216062735586 | [u'dapA'] | 0.0 | 0.0 | nan | |
FACOAE160 | False | False | 0.0293789328922 | 7.25956428312e-05 | [u'tesB'] | 0.0 | 0.0 | nan | |
FACOAE161 | False | False | 0.0228507655338 | 5.64644747037e-05 | [u'tesB'] | 0.0 | 0.0 | nan | |
FACOAE181 | False | False | 0.0117770522398 | 2.91012162063e-05 | [u'tesB'] | 0.0 | 0.0 | nan | |
G1PACT | False | False | 0.0173064007941 | 4.27642928815e-05 | [u'glmU'] | 0.0 | 0.0 | nan | |
GAPD | True | True | 19.3290467436 | 0.0477622716529 | [u'gapA'] | 1.0 | 1.0 | 0.225939104089 | |
GARFT | True | False | 0.0819439612745 | 0.000202484364109 | [u'purN'] | 0.0 | 1.0 | 0.772940755145 | |
GART | False | False | 0.0261712536521 | 6.46694347119e-05 | [u'purT'] | 0.0 | 0.0 | nan | |
GLCS1 | False | False | 0.0406105903609 | 0.000100349182995 | [u'glgA'] | 0.0 | 0.0 | nan | |
GLNS | True | False | 0.420815152487 | 0.00103983853396 | [u'glnA', u'puuA'] | 0.0 | 1.0 | -3.30014468088 | |
GMPS2 | True | True | 0.0572930607008 | 0.00014157173736 | [u'guaA'] | 1.0 | 1.0 | 0.929097348822 | |
HCO3E | False | False | 0.116983370947 | 0.000289067102798 | [u'can', u'cynT'] | 0.0 | 0.0 | nan | |
HISTD | False | False | 0.0222956509067 | 5.50927807981e-05 | [u'hisD'] | 0.0 | 0.0 | nan | |
HSK | True | True | 0.128076472446 | 0.00031647826975 | [u'thrB'] | 1.0 | 1.0 | 0.34485837445 | |
IG3PS | False | False | 0.0222956509067 | 5.50927807981e-05 | [u'hisF', u'hisH'] | 0.0 | 0.0 | nan | |
IMPD | True | True | 0.0572930607005 | 0.00014157173736 | [u'guaB'] | 1.0 | 1.0 | 0.570100565169 | |
IPMD | False | False | 0.10602834647 | 0.00026199712558 | [u'leuB'] | 0.0 | 0.0 | nan | |
IPPS | False | False | 0.10602834647 | 0.00026199712558 | [u'leuA'] | 0.0 | 0.0 | nan | |
Kt2pp | False | False | 0.0449734880605 | 0.000111129947711 | [u'trkG', u'trkA', u'kup', u'trkH', u'sapD', u'kch'] | 0.0 | 0.0 | nan | |
MDH | True | False | 0.170285349565 | 0.000420776835624 | [u'mdh'] | 0.0 | 1.0 | -3.82955472585 | |
METS | False | False | 0.0381810841976 | 9.43458484857e-05 | [u'metE', u'metH'] | 0.0 | 0.0 | nan | |
MTHFC | False | False | 0.208054960745 | 0.000514105930088 | [u'folD'] | 0.0 | 0.0 | nan | |
NAt3pp | False | False | 0.0124922667174 | 3.08685184754e-05 | [u'cmr', u'chaA'] | 0.0 | 0.0 | nan | |
OCBT | False | False | 0.0718634764035 | 0.000177575383175 | [u'argF', u'argI'] | 0.0 | 0.0 | nan | |
PAPSR | False | False | 0.0551962185551 | 0.000136390419032 | [u'cysH', u'trxC', u'trxA'] | 0.0 | 0.0 | nan | |
PFK | False | False | 1.79272979129 | 0.00442985359948 | [u'pfkA', u'pfkB'] | 0.0 | 0.0 | nan | |
PFK_3 | False | False | 0.0859745608558 | 0.000212444016785 | [u'pfkA'] | 0.0 | 0.0 | nan | |
PGCD | False | False | 0.383889615491 | 0.000948595155415 | [u'serA'] | 0.0 | 0.0 | nan | |
PIt2rpp | True | False | 0.229379179846 | 0.000566798292986 | [u'pitA', u'pitB'] | 0.0 | 1.0 | 2.76476054308 | |
POR5 | False | False | 0.0278921131616 | 6.89216961119e-05 | [u'fldB', u'ydbK', u'fldA'] | 0.0 | 0.0 | nan | |
PPC | False | False | 0.7865560074 | 0.00194358791688 | [u'ppc'] | 0.0 | 0.0 | nan | |
PRAGSr | False | False | 0.109078353453 | 0.000269533723944 | [u'purD'] | 0.0 | 0.0 | nan | |
PRAIS | True | False | 0.105376111007 | 0.000260385445098 | [u'purM'] | 0.0 | 1.0 | 0.312342616652 | |
PRASCSi | False | False | 0.105322101164 | 0.000260251986225 | [u'purC'] | 0.0 | 0.0 | nan | |
PRATPP | False | False | 0.0222956509067 | 5.50927807981e-05 | [u'hisI'] | 0.0 | 0.0 | nan | |
PRFGS | False | False | 0.105376111007 | 0.000260385445098 | [u'purL'] | 0.0 | 0.0 | nan | |
PRPPS | False | False | 0.199598304985 | 0.00049320944745 | [u'prs'] | 0.0 | 0.0 | nan | |
PSSA160 | False | False | 0.0106963709769 | 2.6430841783e-05 | [u'pssA'] | 0.0 | 0.0 | nan | |
SHKK | False | False | 0.0900787310712 | 0.000222585463248 | [u'aroK', u'aroL'] | 0.0 | 0.0 | nan | |
SHSL1 | False | False | 0.0378565407447 | 9.35438983034e-05 | [u'metB'] | 0.0 | 0.0 | nan | |
SO4t2pp | False | False | 0.0610294277626 | 0.00015080433848 | [u'ychM'] | 0.0 | 0.0 | nan | |
THD2pp | True | True | 2.90087184238 | 0.00716808391039 | [u'pntB', u'pntA'] | 2.0 | 2.0 | 1.29709104819 |
df = metabolite_panel_nitrate_101['h_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | UGMDDS | False | False | 0.0226804296787 | 3.24407583548e-05 | [u'murF'] | 0.0 | 0.0 | nan |
UDCPDP | False | False | 0.0226804296787 | 3.24407583548e-05 | [u'pgpB', u'ybjG', u'bacA'] | 0.0 | 0.0 | nan | |
UAMAS | False | False | 0.0226804296787 | 3.24407583547e-05 | [u'murC'] | 0.0 | 0.0 | nan | |
UAMAGS | False | False | 0.0226804296787 | 3.24407583547e-05 | [u'murD'] | 0.0 | 0.0 | nan | |
UAGPT3 | False | False | 0.0226804296787 | 3.24407583548e-05 | [u'murG'] | 0.0 | 0.0 | nan | |
UAAGDS | False | False | 0.0226804296787 | 3.24407583547e-05 | [u'murE'] | 0.0 | 0.0 | nan | |
U23GAAT | False | False | 0.0134074179432 | 1.91771854333e-05 | [u'lpxD'] | 0.0 | 0.0 | nan | |
SO4t2pp | False | False | 0.207240914956 | 0.000296425267887 | [u'ychM'] | 0.0 | 0.0 | nan | |
SHSL1 | False | False | 0.128551494395 | 0.000183872529087 | [u'metB'] | 0.0 | 0.0 | nan | |
SHKK | False | False | 0.305885198821 | 0.00043752027452 | [u'aroK', u'aroL'] | 0.0 | 0.0 | nan | |
PSSA181 | False | False | 0.0145604789148 | 2.08264563191e-05 | [u'pssA'] | 0.0 | 0.0 | nan | |
PSSA161 | False | False | 0.0282508162406 | 4.04083130685e-05 | [u'pssA'] | 0.0 | 0.0 | nan | |
PSSA160 | False | False | 0.0363222430408 | 5.19532092681e-05 | [u'pssA'] | 0.0 | 0.0 | nan | |
PRPPS | False | False | 0.714815145596 | 0.00102242972179 | [u'prs'] | 0.0 | 0.0 | nan | |
PRFGS | False | False | 0.35783133578 | 0.00051182098665 | [u'purL'] | 0.0 | 0.0 | nan | |
PRATPP | False | False | 0.0757105426455 | 0.000108291926285 | [u'hisI'] | 0.0 | 0.0 | nan | |
PRASCSi | False | False | 0.357647931646 | 0.000511558656117 | [u'purC'] | 0.0 | 0.0 | nan | |
PRAIS | False | False | 0.35783133578 | 0.00051182098665 | [u'purM'] | 0.0 | 0.0 | nan | |
PRAGSr | False | False | 0.365219796939 | 0.000522389008793 | [u'purD'] | 0.0 | 0.0 | nan | |
PPC | False | False | 2.40574986509 | 0.00344104371658 | [u'ppc'] | 0.0 | 0.0 | nan | |
POR5 | False | False | 0.0913448537573 | 0.00013065432929 | [u'fldB', u'ydbK', u'fldA'] | 0.0 | 0.0 | nan | |
PIt2rpp | True | False | 0.774325572305 | 0.00110754995099 | [u'pitA', u'pitB'] | 0.0 | 1.0 | 1.24142467742 | |
PGSA161 | False | False | 0.0105469713964 | 1.50857702121e-05 | [u'pgsA'] | 0.0 | 0.0 | nan | |
PGSA160 | False | False | 0.0135595693554 | 1.93948139028e-05 | [u'pgsA'] | 0.0 | 0.0 | nan | |
PGL | False | False | 1.26885819325 | 0.00181490045016 | [u'pgl'] | 0.0 | 0.0 | nan | |
PGCD | False | False | 1.34982276632 | 0.00193070743386 | [u'serA'] | 0.0 | 0.0 | nan | |
PFK_3 | False | False | 0.413799568373 | 0.000591874668824 | [u'pfkA'] | 0.0 | 0.0 | nan | |
PFK | False | False | 5.62193955837 | 0.00804129310078 | [u'pfkA', u'pfkB'] | 0.0 | 0.0 | nan | |
PE181abcpp | False | False | 0.0104836435115 | 1.49951897142e-05 | [u'msbA'] | 0.0 | 0.0 | nan | |
PE161abcpp | False | False | 0.0203405876932 | 2.90939854093e-05 | [u'msbA'] | 0.0 | 0.0 | nan | |
PE160abcpp | False | False | 0.0261519491942 | 3.74062165634e-05 | [u'msbA'] | 0.0 | 0.0 | nan | |
PAPSR2 | False | False | 0.0250147981895 | 3.57797023624e-05 | [u'grxA', u'grxC', u'grxB', u'grxD', u'cysH'] | 0.0 | 0.0 | nan | |
PAPSR | False | False | 0.178832729058 | 0.000255791862476 | [u'cysH', u'trxC', u'trxA'] | 0.0 | 0.0 | nan | |
OCBT | False | False | 0.240423602382 | 0.000343887840668 | [u'argF', u'argI'] | 0.0 | 0.0 | nan | |
NAt3pp | False | False | 0.0227993593895 | 3.2610868448e-05 | [u'cmr', u'chaA'] | 0.0 | 0.0 | nan | |
MTHFC | False | False | 0.792935543383 | 0.00113416856374 | [u'folD'] | 0.0 | 0.0 | nan | |
MPTG | False | False | 0.0110634637574 | 1.58245306374e-05 | [u'murJ', u'mrcA', u'mrcB', u'pbpC'] | 0.0 | 0.0 | nan | |
METS | False | False | 0.129653564082 | 0.000185448865026 | [u'metE', u'metH'] | 0.0 | 0.0 | nan | |
MDH | True | False | 8.10514229615 | 0.0115931208705 | [u'mdh'] | 0.0 | 1.0 | -1.73539482182 | |
Kt2pp | False | False | 0.152718895712 | 0.000218440164591 | [u'trkG', u'trkA', u'kup', u'trkH', u'sapD', u'kch'] | 0.0 | 0.0 | nan | |
IPPS | False | False | 0.360046166876 | 0.00051498895134 | [u'leuA'] | 0.0 | 0.0 | nan | |
IPMD | False | False | 0.360046166876 | 0.00051498895134 | [u'leuB'] | 0.0 | 0.0 | nan | |
IMPD | True | True | 0.19455313207 | 0.000278277406295 | [u'guaB'] | 1.0 | 1.0 | 0.635438497562 | |
IG3PS | False | False | 0.0757105426455 | 0.000108291926285 | [u'hisF', u'hisH'] | 0.0 | 0.0 | nan | |
HSK | True | True | 0.434916175774 | 0.000622078627377 | [u'thrB'] | 1.0 | 1.0 | -0.261976732945 | |
HISTD | False | False | 0.0757105426455 | 0.000108291926285 | [u'hisD'] | 0.0 | 0.0 | nan | |
HCO3E | False | False | 0.389010384818 | 0.000556417672421 | [u'can', u'cynT'] | 0.0 | 0.0 | nan | |
GMPS2 | False | False | 0.19455313207 | 0.000278277406295 | [u'guaA'] | 0.0 | 0.0 | nan | |
GMHEPK | False | False | 0.0268148358863 | 3.83543708666e-05 | [u'rfaE'] | 0.0 | 0.0 | nan | |
GLNS | False | False | 1.4289846787 | 0.00204393599729 | [u'glnA', u'puuA'] | 0.0 | 0.0 | nan | |
GLCS1 | False | False | 0.132415747466 | 0.000189399730374 | [u'glgA'] | 0.0 | 0.0 | nan | |
GARFT | True | False | 0.360173584899 | 0.000515171202617 | [u'purN'] | 0.0 | 1.0 | 0.271577409619 | |
GAPD | True | True | 17.2938829399 | 0.0247361573575 | [u'gapA'] | 1.0 | 1.0 | -0.139548915179 | |
G6PDH2r | False | False | 1.27234596105 | 0.00181988914897 | [u'zwf'] | 0.0 | 0.0 | nan | |
G1PACT | False | False | 0.0587682773023 | 8.40587021452e-05 | [u'glmU'] | 0.0 | 0.0 | nan | |
FACOAE181 | False | False | 0.0399919706121 | 5.7202172672e-05 | [u'tesB'] | 0.0 | 0.0 | nan | |
FACOAE161 | False | False | 0.0775955752734 | 0.00011098816656 | [u'tesB'] | 0.0 | 0.0 | nan | |
FACOAE160 | False | False | 0.0997636247925 | 0.000142696046342 | [u'tesB'] | 0.0 | 0.0 | nan | |
FACOAE120 | False | False | 0.033518544858 | 4.79429635834e-05 | [u'tesB'] | 0.0 | 0.0 | nan | |
DUTPDP | False | False | 0.0204006258187 | 2.91798604279e-05 | [u'dut', u'nudI'] | 0.0 | 0.0 | nan | |
DHDPS | False | False | 0.296921424549 | 0.000424699016755 | [u'dapA'] | 0.0 | 0.0 | nan | |
DALAt2pp | True | True | 0.0199704896641 | 2.85646188629e-05 | [u'cycA'] | 1.0 | 1.0 | -0.940038601065 | |
CYSS | False | False | 0.203847527247 | 0.000291571564838 | [u'cysK', u'cysM'] | 0.0 | 0.0 | nan | |
CTPS2 | False | False | 0.127821990058 | 0.000182829088807 | [u'pyrG'] | 0.0 | 0.0 | nan | |
CS | True | False | 8.16163711651 | 0.011673927753 | [u'gltA'] | 0.0 | 1.0 | -2.71754690503 | |
CBMKr | False | False | 0.504114387533 | 0.000721055696949 | [u'yqeA', u'yahI', u'ybcF'] | 0.0 | 0.0 | nan | |
ATPS4rpp | False | False | 39.2837385613 | 0.0561891590234 | [u'atpF', u'atpE', u'atpC', u'atpD', u'atpG', u'atpB', u'atpI', u'atpH', u'atpA'] | 0.0 | 0.0 | nan | |
ASPCT | False | False | 0.263447291456 | 0.00037681957716 | [u'pyrB', u'pyrI'] | 0.0 | 0.0 | nan | |
ASNS2 | False | False | 0.192641781359 | 0.000275543522174 | [u'asnA'] | 0.0 | 0.0 | nan | |
ARGSS | False | False | 0.236385723549 | 0.000338112295261 | [u'argG'] | 0.0 | 0.0 | nan | |
ANS | False | False | 0.045426654564 | 6.49756263197e-05 | [u'trpE', u'trpD'] | 0.0 | 0.0 | nan | |
ALAALAr | False | False | 0.0234508165299 | 3.35426745897e-05 | [u'ddlB', u'ddlA'] | 0.0 | 0.0 | nan | |
AIRC2 | False | False | 0.357647931646 | 0.000511558656117 | [u'purK'] | 0.0 | 0.0 | nan | |
ADSS | True | True | 0.238805342221 | 0.000341573176106 | [u'purA'] | 1.0 | 1.0 | 0.535238843995 | |
ADSK | False | False | 0.203847527247 | 0.000291571564838 | [u'cysC'] | 0.0 | 0.0 | nan | |
ACGS | False | False | 0.269294840319 | 0.000385183568598 | [u'argA'] | 0.0 | 0.0 | nan | |
ACCOAC | False | False | 0.0268452661692 | 3.83978965611e-05 | [u'accB', u'accC', u'accD', u'accA'] | 0.0 | 0.0 | nan | |
consuming | URIt2rpp_reverse | False | False | 0.0108122732148 | 1.5465242396e-05 | [u'xapB'] | 0.0 | 0.0 | nan |
UAPGR | False | False | 0.0226804296787 | 3.24407583547e-05 | [u'murB'] | 0.0 | 0.0 | nan | |
UAGDP | False | False | 0.0587682773023 | 8.40587021452e-05 | [u'glmU'] | 0.0 | 0.0 | nan | |
TRDR | False | False | 0.178832729059 | 0.000255791862478 | [u'trxA', u'trxC', u'trxB'] | 0.0 | 0.0 | nan | |
SULRi | False | False | 0.203847527247 | 0.000291571564838 | [u'cysI', u'cysJ'] | 0.0 | 0.0 | nan | |
SHK3Dr | False | False | 0.30995816683 | 0.000443346009429 | [u'aroE', u'ydiB'] | 0.0 | 0.0 | nan | |
RNTR4c2 | False | False | 0.0204006258167 | 2.9179860425e-05 | [u'fldB', u'fpr', u'nrdD', u'fldA', u'nrdG'] | 0.0 | 0.0 | nan | |
RNTR3c2 | False | False | 0.0210643349499 | 3.01291910996e-05 | [u'fldB', u'nrdD', u'fldA', u'fpr', u'nrdG'] | 0.0 | 0.0 | nan | |
RNTR2c2 | False | False | 0.0210643349503 | 3.01291911002e-05 | [u'nrdG', u'fpr', u'nrdD', u'fldB', u'fldA'] | 0.0 | 0.0 | nan | |
RNTR1c2 | False | False | 0.0204006258178 | 2.91798604266e-05 | [u'fldB', u'nrdD', u'fldA', u'fpr', u'nrdG'] | 0.0 | 0.0 | nan | |
PYK | True | True | 0.20591111489 | 0.000294523199751 | [u'pykF', u'pykA'] | 1.0 | 1.0 | 1.62575576097 | |
PSD181 | False | False | 0.0145604789148 | 2.08264563191e-05 | [u'psd'] | 0.0 | 0.0 | nan | |
PSD161 | False | False | 0.0282508162406 | 4.04083130685e-05 | [u'psd'] | 0.0 | 0.0 | nan | |
PSD160 | False | False | 0.0363222430408 | 5.19532092681e-05 | [u'psd'] | 0.0 | 0.0 | nan | |
PRPPS_reverse | False | False | 0.0152695717711 | 2.18407012134e-05 | [u'prs'] | 0.0 | 0.0 | nan | |
PPNDH | False | False | 0.148056482983 | 0.000211771322473 | [u'pheA'] | 0.0 | 0.0 | nan | |
PIt2rpp_reverse | True | False | 0.0118035555873 | 1.68831146481e-05 | [u'pitA', u'pitB'] | 0.0 | 1.0 | 1.24142467742 | |
P5CR | False | False | 0.176658481131 | 0.000252681945575 | [u'proC'] | 0.0 | 0.0 | nan | |
ORNDC | False | False | 0.0329091167703 | 4.70712733372e-05 | [u'speF', u'speC'] | 0.0 | 0.0 | nan | |
OMPDC | False | False | 0.263447291456 | 0.00037681957716 | [u'pyrF'] | 0.0 | 0.0 | nan | |
NO3R2pp | True | False | 7.72376256058 | 0.0110476176319 | [u'narY', u'narV', u'narG', u'narZ', u'narH', u'narJ', u'narI', u'narW'] | 0.0 | 4.0 | 37.5999970151 | |
NO3R1pp | True | False | 12.2762374394 | 0.0175592110872 | [u'narY', u'narV', u'narZ', u'narG', u'narH', u'narJ', u'narI', u'narW'] | 0.0 | 4.0 | 37.5999970151 | |
NADH18pp | True | False | 0.0228677771053 | 3.27087291419e-05 | [u'nuoN', u'nuoM', u'nuoC', u'nuoE', u'nuoF', u'nuoJ', u'nuoL', u'nuoH', u'nuoA', u'nuoI', u'nuoG', u'nuoB', u'nuoK'] | 0.0 | 25.0 | 8.52569814698 | |
NADH17pp | True | False | 17.5414763258 | 0.0250903004366 | [u'nuoC', u'nuoM', u'nuoN', u'nuoE', u'nuoF', u'nuoB', u'nuoL', u'nuoH', u'nuoI', u'nuoA', u'nuoG', u'nuoJ', u'nuoK'] | 0.0 | 25.0 | 8.52569814698 | |
NADH16pp | True | False | 24.2812947743 | 0.0347305420343 | [u'nuoN', u'nuoM', u'nuoC', u'nuoE', u'nuoF', u'nuoB', u'nuoL', u'nuoK', u'nuoI', u'nuoA', u'nuoG', u'nuoJ', u'nuoH'] | 0.0 | 25.0 | 8.52569814698 | |
MTHFR2 | False | False | 0.129836968217 | 0.000185711195559 | [u'metF'] | 0.0 | 0.0 | nan | |
KARA2 | False | False | 0.236226507674 | 0.000337884562197 | [u'ilvC'] | 0.0 | 0.0 | nan | |
KARA1_reverse | False | False | 0.707074834399 | 0.00101135843396 | [u'ilvC'] | 0.0 | 0.0 | nan | |
IGPS | False | False | 0.045426654564 | 6.49756263197e-05 | [u'trpC'] | 0.0 | 0.0 | nan | |
HSDy_reverse | True | True | 0.567682164731 | 0.000811979322668 | [u'thrA', u'metL'] | 1.0 | 1.0 | -0.283006387364 | |
HACD8 | True | False | 0.045883372823 | 6.56288893701e-05 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD7 | True | False | 0.226172797128 | 0.000323504323419 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD6 | True | False | 0.227792607653 | 0.00032582120553 | [u'fadJ', u'fadB'] | 0.0 | 2.0 | -12.8696463866 | |
HACD5 | True | False | 0.261193760388 | 0.000373596258295 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD4 | True | False | 0.26213101072 | 0.000374936846281 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD3 | True | False | 0.261547608995 | 0.000374102382621 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD2 | True | False | 0.262947584332 | 0.000376104825354 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD1 | True | False | 0.260720034653 | 0.000372918668748 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
GTHOr | False | False | 0.0303608912377 | 4.34264407698e-05 | [u'gor'] | 0.0 | 0.0 | nan | |
GMHEPAT | False | False | 0.0268148358863 | 3.83543708666e-05 | [u'rfaE'] | 0.0 | 0.0 | nan | |
GLUt2rpp_reverse | False | False | 0.0166091652521 | 2.37567772768e-05 | [u'gltP'] | 0.0 | 0.0 | nan | |
GLUDy_reverse | False | False | 6.87445671995 | 0.00983282029622 | [u'gdhA'] | 0.0 | 0.0 | nan | |
GLGC | False | False | 0.132415747466 | 0.000189399730374 | [u'glgC'] | 0.0 | 0.0 | nan | |
GALUi | False | False | 0.0268148358863 | 3.83543708665e-05 | [u'galU'] | 0.0 | 0.0 | nan | |
G5SD | False | False | 0.176658481131 | 0.000252681945575 | [u'proA'] | 0.0 | 0.0 | nan | |
G3PD2_reverse | False | False | 0.136812803847 | 0.000195689022311 | [u'gpsA'] | 0.0 | 0.0 | nan | |
FADRx | False | False | 1.65232239061 | 0.00236338518084 | [u'fre'] | 0.0 | 0.0 | nan | |
DHORTS_reverse | False | False | 0.270744246088 | 0.000387256713727 | [u'pyrC'] | 0.0 | 0.0 | nan | |
DHFR | False | False | 0.0236006886215 | 3.37570428524e-05 | [u'folA', u'folM'] | 0.0 | 0.0 | nan | |
DHDPRy | False | False | 0.296921424549 | 0.000424699016755 | [u'dapB'] | 0.0 | 0.0 | nan | |
DASYN181 | False | False | 0.0199959853061 | 2.8601086336e-05 | [u'cdsA'] | 0.0 | 0.0 | nan | |
DASYN161 | False | False | 0.038797787637 | 5.54940832806e-05 | [u'cdsA'] | 0.0 | 0.0 | nan | |
DASYN160 | False | False | 0.0498818123964 | 7.13480231711e-05 | [u'cdsA'] | 0.0 | 0.0 | nan | |
DAPDC | False | False | 0.27424099487 | 0.000392258258401 | [u'lysA'] | 0.0 | 0.0 | nan | |
ASAD_reverse | False | False | 0.866277161428 | 0.00123907211901 | [u'asd'] | 0.0 | 0.0 | nan | |
AGPR_reverse | False | False | 0.273278559091 | 0.000390881646626 | [u'argC'] | 0.0 | 0.0 | nan | |
ACLS | False | False | 0.698694088135 | 0.000999371105316 | [u'ilvB', u'ilvH', u'ilvN', u'ilvI'] | 0.0 | 0.0 | nan | |
ACHBS | False | False | 0.232179765055 | 0.000332096338548 | [u'ilvB', u'ilvH', u'ilvN', u'ilvI'] | 0.0 | 0.0 | nan | |
3OAS140 | True | True | 0.0268148358864 | 3.83543708667e-05 | [u'fabF', u'fabB'] | 1.0 | 1.0 | 0.445013595973 | |
3OAR140 | False | False | 0.0319789704932 | 4.57408465756e-05 | [u'fabG'] | 0.0 | 0.0 | nan |
df = metabolite_panel_anaerobic_101['nadh_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | PPND | False | False | 0.0325066598811 | 8.03242881225e-05 | [u'tyrA'] | 0.0 | 0.0 | nan |
PGCD | False | False | 0.383889615491 | 0.000948595155415 | [u'serA'] | 0.0 | 0.0 | nan | |
MDH | True | False | 0.170285349565 | 0.000420776835624 | [u'mdh'] | 0.0 | 1.0 | -3.82955472585 | |
IPMD | False | False | 0.10602834647 | 0.00026199712558 | [u'leuB'] | 0.0 | 0.0 | nan | |
IMPD | True | True | 0.0572930607005 | 0.00014157173736 | [u'guaB'] | 1.0 | 1.0 | 0.570100565169 | |
HISTD | False | False | 0.0222956509067 | 5.50927807981e-05 | [u'hisD'] | 0.0 | 0.0 | nan | |
GAPD | True | True | 19.3290467436 | 0.0477622716529 | [u'gapA'] | 1.0 | 1.0 | 0.225939104089 | |
consuming | THD2pp | True | True | 2.90087184238 | 0.00716808391039 | [u'pntB', u'pntA'] | 2.0 | 2.0 | 1.29709104819 |
MTHFR2 | False | False | 0.0382350940411 | 9.44793073599e-05 | [u'metF'] | 0.0 | 0.0 | nan | |
HACD8 | True | False | 0.0143419864279 | 3.54391947465e-05 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD7 | True | False | 0.0673410991948 | 0.000166400542966 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD6 | True | False | 0.0679896617665 | 0.000168003147695 | [u'fadJ', u'fadB'] | 0.0 | 2.0 | -6.44117175826 | |
HACD5 | True | False | 0.0780245278058 | 0.000192799404031 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD4 | True | False | 0.0785905927577 | 0.0001941981563 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD3 | True | False | 0.078168917303 | 0.000193156191951 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD2 | True | False | 0.0797551048851 | 0.000197075677645 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
HACD1 | True | False | 0.0777672212243 | 0.000192163596843 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -6.44117175826 | |
FADRx | False | False | 0.486584852294 | 0.00120235613301 | [u'fre'] | 0.0 | 0.0 | nan | |
ALCD2x_reverse | True | False | 8.0873620921 | 0.0199839542178 | [u'adhP', u'adhE', u'frmA'] | 0.0 | 1.0 | 0.587546853664 | |
ACALD_reverse | True | False | 8.08683403253 | 0.0199826493772 | [u'adhE', u'mhpF'] | 0.0 | 1.0 | 0.587546853664 |
df = metabolite_panel_nitrate_101['nadh_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | PPND | False | False | 0.110384615795 | 0.000157887689863 | [u'tyrA'] | 0.0 | 0.0 | nan |
PGCD | False | False | 1.34982276632 | 0.00193070743386 | [u'serA'] | 0.0 | 0.0 | nan | |
PDH | True | False | 10.5333215141 | 0.0150662462198 | [u'aceE', u'aceF', u'lpd'] | 0.0 | 1.0 | -1.26350135724 | |
MDH | True | False | 8.10514229615 | 0.0115931208705 | [u'mdh'] | 0.0 | 1.0 | -1.73539482182 | |
IPMD | False | False | 0.360046166876 | 0.00051498895134 | [u'leuB'] | 0.0 | 0.0 | nan | |
IMPD | True | True | 0.19455313207 | 0.000278277406295 | [u'guaB'] | 1.0 | 1.0 | 0.635438497562 | |
HISTD | False | False | 0.0757105426455 | 0.000108291926285 | [u'hisD'] | 0.0 | 0.0 | nan | |
GLYCL | True | False | 0.0462281224084 | 6.61219989871e-05 | [u'gcvT', u'gcvP', u'lpd', u'gcvH'] | 0.0 | 1.0 | -1.26350135724 | |
GAPD | True | True | 17.2938829399 | 0.0247361573575 | [u'gapA'] | 1.0 | 1.0 | -0.139548915179 | |
AKGDH | True | False | 7.26670224929 | 0.0103938653299 | [u'sucA', u'lpd', u'sucB'] | 0.0 | 3.0 | -7.29009006112 | |
consuming | NADH18pp | True | False | 0.0228677771053 | 3.27087291419e-05 | [u'nuoN', u'nuoM', u'nuoC', u'nuoE', u'nuoF', u'nuoJ', u'nuoL', u'nuoH', u'nuoA', u'nuoI', u'nuoG', u'nuoB', u'nuoK'] | 0.0 | 25.0 | 8.52569814698 |
NADH17pp | True | False | 17.5414763258 | 0.0250903004366 | [u'nuoC', u'nuoM', u'nuoN', u'nuoE', u'nuoF', u'nuoB', u'nuoL', u'nuoH', u'nuoI', u'nuoA', u'nuoG', u'nuoJ', u'nuoK'] | 0.0 | 25.0 | 8.52569814698 | |
NADH16pp | True | False | 24.2812947743 | 0.0347305420343 | [u'nuoN', u'nuoM', u'nuoC', u'nuoE', u'nuoF', u'nuoB', u'nuoL', u'nuoK', u'nuoI', u'nuoA', u'nuoG', u'nuoJ', u'nuoH'] | 0.0 | 25.0 | 8.52569814698 | |
MTHFR2 | False | False | 0.129836968217 | 0.000185711195559 | [u'metF'] | 0.0 | 0.0 | nan | |
HACD8 | True | False | 0.045883372823 | 6.56288893701e-05 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD7 | True | False | 0.226172797128 | 0.000323504323419 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD6 | True | False | 0.227792607653 | 0.00032582120553 | [u'fadJ', u'fadB'] | 0.0 | 2.0 | -12.8696463866 | |
HACD5 | True | False | 0.261193760388 | 0.000373596258295 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD4 | True | False | 0.26213101072 | 0.000374936846281 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD3 | True | False | 0.261547608995 | 0.000374102382621 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD2 | True | False | 0.262947584332 | 0.000376104825354 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
HACD1 | True | False | 0.260720034653 | 0.000372918668748 | [u'fadB', u'fadJ'] | 0.0 | 2.0 | -12.8696463866 | |
FADRx | False | False | 1.65232239061 | 0.00236338518084 | [u'fre'] | 0.0 | 0.0 | nan |
df = metabolite_panel_anaerobic_101['nadph_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | THD2pp | True | True | 2.90087184238 | 0.00716808391039 | [u'pntB', u'pntA'] | 2.0 | 2.0 | 1.29709104819 |
MTHFD | False | False | 0.208565525879 | 0.000515367541741 | [u'folD'] | 0.0 | 0.0 | nan | |
ICDHyr | True | False | 0.268733116588 | 0.000664042272072 | [u'icd'] | 0.0 | 1.0 | -2.11702427496 | |
consuming | TRDR | False | False | 0.055196218587 | 0.00013639041911 | [u'trxA', u'trxC', u'trxB'] | 0.0 | 0.0 | nan |
SULRi | False | False | 0.0600301245591 | 0.000148335050072 | [u'cysI', u'cysJ'] | 0.0 | 0.0 | nan | |
SHK3Dr | False | False | 0.092275546831 | 0.000228013817397 | [u'aroE', u'ydiB'] | 0.0 | 0.0 | nan | |
P5CR | False | False | 0.0520233469143 | 0.000128550220845 | [u'proC'] | 0.0 | 0.0 | nan | |
KARA2 | False | False | 0.070918719906 | 0.000175240880234 | [u'ilvC'] | 0.0 | 0.0 | nan | |
KARA1_reverse | False | False | 0.208950714224 | 0.000516319346071 | [u'ilvC'] | 0.0 | 0.0 | nan | |
HSDy_reverse | False | False | 0.167898854474 | 0.000414879781914 | [u'thrA', u'metL'] | 0.0 | 0.0 | nan | |
GLUDy_reverse | False | False | 2.01170910993 | 0.00497095372935 | [u'gdhA'] | 0.0 | 0.0 | nan | |
G5SD | False | False | 0.0520233469134 | 0.000128550220843 | [u'proA'] | 0.0 | 0.0 | nan | |
G3PD2_reverse | False | False | 0.0414638909066 | 0.000102457697347 | [u'gpsA'] | 0.0 | 0.0 | nan | |
DHDPRy | False | False | 0.0874390302466 | 0.000216062735586 | [u'dapB'] | 0.0 | 0.0 | nan | |
ASAD_reverse | False | False | 0.255916923253 | 0.00063237332762 | [u'asd'] | 0.0 | 0.0 | nan | |
AGPR_reverse | False | False | 0.0814776053093 | 0.000201331993762 | [u'argC'] | 0.0 | 0.0 | nan | |
3OAR140 | False | False | 0.0110742045993 | 2.73644725178e-05 | [u'fabG'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['nadph_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | MTHFD | False | False | 0.793961011131 | 0.00113563533275 | [u'folD'] | 0.0 | 0.0 | nan |
ICDHyr | True | False | 8.16896134529 | 0.0116844039009 | [u'icd'] | 0.0 | 1.0 | -1.34545454214 | |
GND | False | False | 1.26885819325 | 0.00181490045016 | [u'gnd'] | 0.0 | 0.0 | nan | |
G6PDH2r | False | False | 1.27234596105 | 0.00181988914897 | [u'zwf'] | 0.0 | 0.0 | nan | |
consuming | UAPGR | False | False | 0.0226804296787 | 3.24407583547e-05 | [u'murB'] | 0.0 | 0.0 | nan |
TRDR | False | False | 0.178832729059 | 0.000255791862478 | [u'trxA', u'trxC', u'trxB'] | 0.0 | 0.0 | nan | |
SULRi | False | False | 0.203847527247 | 0.000291571564838 | [u'cysI', u'cysJ'] | 0.0 | 0.0 | nan | |
SHK3Dr | False | False | 0.30995816683 | 0.000443346009429 | [u'aroE', u'ydiB'] | 0.0 | 0.0 | nan | |
P5CR | False | False | 0.176658481131 | 0.000252681945575 | [u'proC'] | 0.0 | 0.0 | nan | |
KARA2 | False | False | 0.236226507674 | 0.000337884562197 | [u'ilvC'] | 0.0 | 0.0 | nan | |
KARA1_reverse | False | False | 0.707074834399 | 0.00101135843396 | [u'ilvC'] | 0.0 | 0.0 | nan | |
HSDy_reverse | True | True | 0.567682164731 | 0.000811979322668 | [u'thrA', u'metL'] | 1.0 | 1.0 | -0.283006387364 | |
GTHOr | False | False | 0.0303608912377 | 4.34264407698e-05 | [u'gor'] | 0.0 | 0.0 | nan | |
GLUDy_reverse | False | False | 6.87445671995 | 0.00983282029622 | [u'gdhA'] | 0.0 | 0.0 | nan | |
G5SD | False | False | 0.176658481131 | 0.000252681945575 | [u'proA'] | 0.0 | 0.0 | nan | |
G3PD2_reverse | False | False | 0.136812803847 | 0.000195689022311 | [u'gpsA'] | 0.0 | 0.0 | nan | |
DHFR | False | False | 0.0236006886215 | 3.37570428524e-05 | [u'folA', u'folM'] | 0.0 | 0.0 | nan | |
DHDPRy | False | False | 0.296921424549 | 0.000424699016755 | [u'dapB'] | 0.0 | 0.0 | nan | |
ASAD_reverse | False | False | 0.866277161428 | 0.00123907211901 | [u'asd'] | 0.0 | 0.0 | nan | |
AGPR_reverse | False | False | 0.273278559091 | 0.000390881646626 | [u'argC'] | 0.0 | 0.0 | nan | |
3OAR140 | False | False | 0.0319789704932 | 4.57408465756e-05 | [u'fabG'] | 0.0 | 0.0 | nan |
df = metabolite_panel_anaerobic_101['pyr_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | VPAMTr | False | False | 0.0142276738652 | 3.51567272382e-05 | [u'avtA'] | 0.0 | 0.0 | nan |
PYK | True | True | 0.0975618664448 | 0.000241076367081 | [u'pykF', u'pykA'] | 1.0 | 1.0 | 3.6770040631 | |
GLCptspp | True | True | 10.0 | 0.0247101019964 | [u'ptsG', u'manX', u'crr', u'ptsH', u'manY', u'manZ', u'ptsI', u'malX'] | 1.0 | 1.0 | 1.14780003733 | |
DHAPT | True | True | 7.86463461894 | 0.0194335923599 | [u'dhaL', u'dhaK', u'ptsI', u'ptsH', u'dhaM'] | 2.0 | 2.0 | 3.43769754423 | |
CYSTL | False | False | 0.0378565407447 | 9.35438983034e-05 | [u'metC', u'malY'] | 0.0 | 0.0 | nan | |
ANS | False | False | 0.0133774874225 | 3.30559078666e-05 | [u'trpE', u'trpD'] | 0.0 | 0.0 | nan | |
consuming | VPAMTr_reverse | False | False | 0.0128897769482 | 3.18507703102e-05 | [u'avtA'] | 0.0 | 0.0 | nan |
TRPAS2_reverse | False | False | 0.0157349180021 | 3.88811428739e-05 | [u'tnaA'] | 0.0 | 0.0 | nan | |
POR5 | False | False | 0.0278921131616 | 6.89216961119e-05 | [u'fldB', u'ydbK', u'fldA'] | 0.0 | 0.0 | nan | |
PFL | True | False | 17.2725055582 | 0.0426805374078 | [u'pflA', u'pflB', u'tdcE', u'pflD', u'yfiD', u'pflC'] | 0.0 | 2.0 | 4.05181918871 | |
DHDPS | False | False | 0.0874390302466 | 0.000216062735586 | [u'dapA'] | 0.0 | 0.0 | nan | |
ALATA_L_reverse | False | False | 0.139767033075 | 0.000345365764303 | [u'yfdZ', u'yfbQ'] | 0.0 | 0.0 | nan | |
ACLS | False | False | 0.205755221604 | 0.000508423251214 | [u'ilvB', u'ilvH', u'ilvN', u'ilvI'] | 0.0 | 0.0 | nan | |
ACHBS | False | False | 0.0683735554976 | 0.00016895175302 | [u'ilvB', u'ilvH', u'ilvN', u'ilvI'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['pyr_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | VPAMTr | False | False | 0.0329391586556 | 4.71142434906e-05 | [u'avtA'] | 0.0 | 0.0 | nan |
PYK | True | True | 0.20591111489 | 0.000294523199751 | [u'pykF', u'pykA'] | 1.0 | 1.0 | 1.62575576097 | |
GLCptspp | True | True | 10.0 | 0.0143034143596 | [u'ptsG', u'manX', u'crr', u'ptsH', u'manY', u'manZ', u'ptsI', u'malX'] | 1.0 | 2.0 | 1.35151438926 | |
DHAPT | False | False | 2.66943102851 | 0.0038181978105 | [u'dhaL', u'dhaK', u'ptsI', u'ptsH', u'dhaM'] | 0.0 | 0.0 | nan | |
CYSTL | False | False | 0.128551494395 | 0.000183872529087 | [u'metC', u'malY'] | 0.0 | 0.0 | nan | |
ANS | False | False | 0.045426654564 | 6.49756263197e-05 | [u'trpE', u'trpD'] | 0.0 | 0.0 | nan | |
consuming | VPAMTr_reverse | False | False | 0.028502724666 | 4.07686281274e-05 | [u'avtA'] | 0.0 | 0.0 | nan |
TRPAS2_reverse | False | False | 0.0518601544007 | 7.41777277143e-05 | [u'tnaA'] | 0.0 | 0.0 | nan | |
POR5 | False | False | 0.0913448537573 | 0.00013065432929 | [u'fldB', u'ydbK', u'fldA'] | 0.0 | 0.0 | nan | |
PDH | True | False | 10.5333215141 | 0.0150662462198 | [u'aceE', u'aceF', u'lpd'] | 0.0 | 1.0 | -1.26350135724 | |
DHDPS | False | False | 0.296921424549 | 0.000424699016755 | [u'dapA'] | 0.0 | 0.0 | nan | |
ALATA_L_reverse | False | False | 0.460952235608 | 0.000659319082586 | [u'yfdZ', u'yfbQ'] | 0.0 | 0.0 | nan | |
ACLS | False | False | 0.698694088135 | 0.000999371105316 | [u'ilvB', u'ilvH', u'ilvN', u'ilvI'] | 0.0 | 0.0 | nan | |
ACHBS | False | False | 0.232179765055 | 0.000332096338548 | [u'ilvB', u'ilvH', u'ilvN', u'ilvI'] | 0.0 | 0.0 | nan |
df = metabolite_panel_anaerobic_101['g3p_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | TRPS3 | False | False | 0.0133774874221 | 3.30559078656e-05 | [u'trpA', u'trpB'] | 0.0 | 0.0 | nan |
TPI | False | False | 9.70568161222 | 0.0239828382583 | [u'tpiA'] | 0.0 | 0.0 | nan | |
TALA_reverse | False | False | 0.139259584127 | 0.000344111852776 | [u'talB', u'talA'] | 0.0 | 0.0 | nan | |
FBA | False | False | 1.79504890053 | 0.00443558414208 | [u'fbaB', u'fbaA', u'ydjI'] | 0.0 | 0.0 | nan | |
F6PA | False | False | 7.86689298566 | 0.0194391728071 | [u'fsaB', u'fsaA'] | 0.0 | 0.0 | nan | |
consuming | TKT2_reverse | False | False | 0.14421789557 | 0.000356363890924 | [u'tktB', u'tktA'] | 0.0 | 0.0 | nan |
TKT1_reverse | False | False | 0.0456504885766 | 0.000112802822892 | [u'tktB', u'tktA'] | 0.0 | 0.0 | nan | |
GAPD | True | True | 19.3290467436 | 0.0477622716529 | [u'gapA'] | 1.0 | 1.0 | 0.225939104089 |
df = metabolite_panel_nitrate_101['g3p_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | TRPS3 | False | False | 0.0454266545637 | 6.49756263193e-05 | [u'trpA', u'trpB'] | 0.0 | 0.0 | nan |
TPI | False | False | 8.57380207397 | 0.0122634643701 | [u'tpiA'] | 0.0 | 0.0 | nan | |
TKT1 | False | False | 0.280092326935 | 0.000400627661108 | [u'tktB', u'tktA'] | 0.0 | 0.0 | nan | |
TALA_reverse | False | False | 0.179351050481 | 0.000256533239086 | [u'talB', u'talA'] | 0.0 | 0.0 | nan | |
FBA | False | False | 5.62628724152 | 0.00804751177213 | [u'fbaB', u'fbaA', u'ydjI'] | 0.0 | 0.0 | nan | |
F6PA | True | True | 2.67476083014 | 0.00382582124662 | [u'fsaB', u'fsaA'] | 1.0 | 1.0 | 0.349968647141 | |
consuming | TKT2_reverse | False | False | 0.0616290585778 | 8.81505961427e-05 | [u'tktB', u'tktA'] | 0.0 | 0.0 | nan |
TALA | False | False | 0.0151481520909 | 2.16670296138e-05 | [u'talB', u'talA'] | 0.0 | 0.0 | nan | |
GAPD | True | True | 17.2938829399 | 0.0247361573575 | [u'gapA'] | 1.0 | 1.0 | -0.139548915179 |
df = metabolite_panel_anaerobic_101['akg_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | VALTA_reverse | False | False | 0.101591006016 | 0.000251032412059 | [u'ilvE'] | 0.0 | 0.0 | nan |
TYRTA_reverse | False | False | 0.034235624541 | 8.4596577432e-05 | [u'aspC', u'tyrB'] | 0.0 | 0.0 | nan | |
SDPTA_reverse | False | False | 0.0909597798008 | 0.000224762543645 | [u'argD'] | 0.0 | 0.0 | nan | |
PSERT | False | False | 0.383889615491 | 0.000948595155415 | [u'serC'] | 0.0 | 0.0 | nan | |
PHETA1_reverse | False | False | 0.0461196072785 | 0.000113962019989 | [u'tyrB', u'ilvE', u'aspC'] | 0.0 | 0.0 | nan | |
LEUTAi | False | False | 0.10602834647 | 0.00026199712558 | [u'tyrB', u'ilvE'] | 0.0 | 0.0 | nan | |
ILETA_reverse | False | False | 0.0706123672895 | 0.000174483879794 | [u'ilvE'] | 0.0 | 0.0 | nan | |
ICDHyr | True | False | 0.268733116588 | 0.000664042272072 | [u'icd'] | 0.0 | 1.0 | -2.11702427496 | |
HSTPT | False | False | 0.0222956509067 | 5.50927807981e-05 | [u'hisC'] | 0.0 | 0.0 | nan | |
ASPTA_reverse | False | False | 0.696537990833 | 0.00172115247979 | [u'aspC'] | 0.0 | 0.0 | nan | |
ALATA_L_reverse | False | False | 0.139767033075 | 0.000345365764303 | [u'yfdZ', u'yfbQ'] | 0.0 | 0.0 | nan | |
ACOTA_reverse | True | True | 0.0810751379244 | 0.000200337492749 | [u'astC', u'argD'] | 1.0 | 1.0 | -3.19054636273 | |
consuming | GLUDy_reverse | False | False | 2.01170910993 | 0.00497095372935 | [u'gdhA'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['akg_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | VALTA_reverse | False | False | 0.340184087268 | 0.000486579395871 | [u'ilvE'] | 0.0 | 0.0 | nan |
TYRTA_reverse | False | False | 0.113572259682 | 0.000162447108998 | [u'aspC', u'tyrB'] | 0.0 | 0.0 | nan | |
SDPTA_reverse | False | False | 0.302649873828 | 0.000432892655123 | [u'argD'] | 0.0 | 0.0 | nan | |
PSERT | False | False | 1.34982276632 | 0.00193070743386 | [u'serC'] | 0.0 | 0.0 | nan | |
PHETA1_reverse | False | False | 0.152028655838 | 0.000217452885898 | [u'tyrB', u'ilvE', u'aspC'] | 0.0 | 0.0 | nan | |
LEUTAi | False | False | 0.360046166876 | 0.00051498895134 | [u'tyrB', u'ilvE'] | 0.0 | 0.0 | nan | |
ILETA_reverse | False | False | 0.235868931421 | 0.000337373106066 | [u'ilvE'] | 0.0 | 0.0 | nan | |
ICDHyr | True | False | 8.16896134529 | 0.0116844039009 | [u'icd'] | 0.0 | 1.0 | -1.34545454214 | |
HSTPT | False | False | 0.0757105426455 | 0.000108291926285 | [u'hisC'] | 0.0 | 0.0 | nan | |
ASPTA_reverse | False | False | 2.35397083122 | 0.00336698201892 | [u'aspC'] | 0.0 | 0.0 | nan | |
ALATA_L_reverse | False | False | 0.460952235608 | 0.000659319082586 | [u'yfdZ', u'yfbQ'] | 0.0 | 0.0 | nan | |
ACOTA_reverse | True | True | 0.272126141606 | 0.000389233296146 | [u'astC', u'argD'] | 1.0 | 1.0 | -6.6019843564 | |
consuming | GLUDy_reverse | False | False | 6.87445671995 | 0.00983282029622 | [u'gdhA'] | 0.0 | 0.0 | nan |
AKGDH | True | False | 7.26670224929 | 0.0103938653299 | [u'sucA', u'lpd', u'sucB'] | 0.0 | 3.0 | -7.29009006112 |
df = metabolite_panel_anaerobic_101['fum_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | ARGSL | False | False | 0.0715707540573 | 0.000176852063272 | [u'argH'] | 0.0 | 0.0 | nan |
ADSL2r | False | False | 0.108042282683 | 0.000266973582502 | [u'purB'] | 0.0 | 0.0 | nan | |
ADSL1r | False | False | 0.0723627530142 | 0.000178809100773 | [u'purB'] | 0.0 | 0.0 | nan | |
consuming | FUM | True | False | 0.170193921268 | 0.000420550915371 | [u'fumA', u'fumB', u'fumC'] | 0.0 | 2.0 | -4.87556892288 |
FRD2 | True | False | 0.0107235883687 | 2.64980962359e-05 | [u'frdD', u'frdC', u'frdB', u'frdA'] | 0.0 | 4.0 | 16.042983826 |
df = metabolite_panel_nitrate_101['fum_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | SUCDi | True | False | 7.37561608879 | 0.0105496493075 | [u'sdhD', u'sdhA', u'sdhC', u'sdhB'] | 0.0 | 4.0 | -23.717233222 |
ARGSL | False | False | 0.239589181552 | 0.000342694333981 | [u'argH'] | 0.0 | 0.0 | nan | |
ADSL2r | False | False | 0.361005767238 | 0.0005163615075 | [u'purB'] | 0.0 | 0.0 | nan | |
ADSL1r | False | False | 0.242149237614 | 0.000346356088244 | [u'purB'] | 0.0 | 0.0 | nan | |
consuming | FUM | True | False | 8.10559167514 | 0.0115937636359 | [u'fumA', u'fumB', u'fumC'] | 0.0 | 1.0 | -3.16365981899 |
FRD3 | False | False | 0.0229141827043 | 3.2775104993e-05 | [u'frdD', u'frdC', u'frdB', u'frdA'] | 0.0 | 0.0 | nan | |
FRD2 | False | False | 0.0644942124367 | 9.22487444275e-05 | [u'frdD', u'frdC', u'frdB', u'frdA'] | 0.0 | 0.0 | nan |
df = metabolite_panel_anaerobic_101['succ_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | SHSL1 | False | False | 0.0378565407447 | 9.35438983034e-05 | [u'metB'] | 0.0 | 0.0 | nan |
SDPDS | False | False | 0.0874390302466 | 0.000216062735586 | [u'dapE'] | 0.0 | 0.0 | nan | |
FRD2 | True | False | 0.0107235883687 | 2.64980962359e-05 | [u'frdD', u'frdC', u'frdB', u'frdA'] | 0.0 | 4.0 | 16.042983826 | |
consuming | SUCOAS | True | False | 0.119108219478 | 0.000294317625192 | [u'sucD', u'sucC'] | 0.0 | 2.0 | -9.11368614951 |
df = metabolite_panel_nitrate_101['succ_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | SUCOAS_reverse | True | False | 6.84727218826 | 0.00979393713413 | [u'sucD', u'sucC'] | 0.0 | 2.0 | -5.36626496942 |
SHSL1 | False | False | 0.128551494395 | 0.000183872529087 | [u'metB'] | 0.0 | 0.0 | nan | |
SDPDS | False | False | 0.296921424549 | 0.000424699016755 | [u'dapE'] | 0.0 | 0.0 | nan | |
FRD3 | False | False | 0.0229141827043 | 3.2775104993e-05 | [u'frdD', u'frdC', u'frdB', u'frdA'] | 0.0 | 0.0 | nan | |
FRD2 | False | False | 0.0644942124367 | 9.22487444275e-05 | [u'frdD', u'frdC', u'frdB', u'frdA'] | 0.0 | 0.0 | nan | |
consuming | SUCDi | True | False | 7.37561608879 | 0.0105496493075 | [u'sdhD', u'sdhA', u'sdhC', u'sdhB'] | 0.0 | 4.0 | -23.717233222 |
df = metabolite_panel_anaerobic_101['mal__L_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | FUM | True | False | 0.170193921268 | 0.000420550915371 | [u'fumA', u'fumB', u'fumC'] | 0.0 | 2.0 | -4.87556892288 |
consuming | MDH | True | False | 0.170285349565 | 0.000420776835624 | [u'mdh'] | 0.0 | 1.0 | -3.82955472585 |
df = metabolite_panel_nitrate_101['mal__L_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | FUM | True | False | 8.10559167514 | 0.0115937636359 | [u'fumA', u'fumB', u'fumC'] | 0.0 | 1.0 | -3.16365981899 |
consuming | MDH | True | False | 8.10514229615 | 0.0115931208705 | [u'mdh'] | 0.0 | 1.0 | -1.73539482182 |
df = metabolite_panel_anaerobic_101['accoa_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | POR5 | False | False | 0.0278921131616 | 6.89216961119e-05 | [u'fldB', u'ydbK', u'fldA'] | 0.0 | 0.0 | nan |
PFL | True | False | 17.2725055582 | 0.0426805374078 | [u'pflA', u'pflB', u'tdcE', u'pflD', u'yfiD', u'pflC'] | 0.0 | 2.0 | 4.05181918871 | |
consuming | SERAT | False | False | 0.0621247827791 | 0.000153510971898 | [u'cysE'] | 0.0 | 0.0 | nan |
PTAr | True | True | 8.09408926698 | 0.0200005771355 | [u'eutD', u'pta'] | 1.0 | 1.0 | 2.70785002487 | |
IPPS | False | False | 0.10602834647 | 0.00026199712558 | [u'leuA'] | 0.0 | 0.0 | nan | |
G1PACT | False | False | 0.0173064007941 | 4.27642928815e-05 | [u'glmU'] | 0.0 | 0.0 | nan | |
CS | True | False | 0.263545269736 | 0.000651223049586 | [u'gltA'] | 0.0 | 1.0 | -3.39561619493 | |
ACGS | False | False | 0.0793034040047 | 0.000195959520162 | [u'argA'] | 0.0 | 0.0 | nan | |
ACALD_reverse | True | False | 8.08683403253 | 0.0199826493772 | [u'adhE', u'mhpF'] | 0.0 | 1.0 | 0.587546853664 | |
ACACT8r_reverse | True | False | 0.014118292196 | 3.48864440178e-05 | [u'fadA', u'fadI'] | 0.0 | 1.0 | -1.2824707151 | |
ACACT7r | True | False | 0.0655974045685 | 0.000162091855759 | [u'fadA', u'fadI'] | 0.0 | 1.0 | -1.2824707151 | |
ACACT6r | True | False | 0.067704010325 | 0.00016729730007 | [u'fadA', u'fadI'] | 0.0 | 1.0 | -1.2824707151 | |
ACACT5r | True | False | 0.0774503269774 | 0.000191380547927 | [u'fadA', u'fadI'] | 0.0 | 1.0 | -1.2824707151 | |
ACACT4r | True | False | 0.0776014067748 | 0.000191753867647 | [u'fadA', u'fadI'] | 0.0 | 1.0 | -1.2824707151 | |
ACACT3r | True | False | 0.0779498774525 | 0.000192614942246 | [u'fadA', u'fadI'] | 0.0 | 1.0 | -1.2824707151 | |
ACACT2r | True | False | 0.0774134900732 | 0.000191289523561 | [u'fadA', u'fadI'] | 0.0 | 1.0 | -1.2824707151 | |
ACACT1r | True | False | 0.0778520913006 | 0.000192373311667 | [u'fadA', u'fadI', u'atoB'] | 0.0 | 1.0 | -1.2824707151 |
df = metabolite_panel_nitrate_101['accoa_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | PTAr_reverse | True | True | 0.441393018473 | 0.000631342723863 | [u'eutD', u'pta'] | 1.0 | 1.0 | 0.975672096934 |
POR5 | False | False | 0.0913448537573 | 0.00013065432929 | [u'fldB', u'ydbK', u'fldA'] | 0.0 | 0.0 | nan | |
PDH | True | False | 10.5333215141 | 0.0150662462198 | [u'aceE', u'aceF', u'lpd'] | 0.0 | 1.0 | -1.26350135724 | |
ACS | True | True | 0.0607009136363 | 8.68230319743e-05 | [u'acs'] | 1.0 | 1.0 | -5.52079862311 | |
consuming | SERAT | False | False | 0.207691823731 | 0.000297070221391 | [u'cysE'] | 0.0 | 0.0 | nan |
PTAr | True | True | 0.0155441466014 | 2.22334369706e-05 | [u'eutD', u'pta'] | 1.0 | 1.0 | 0.975672096934 | |
IPPS | False | False | 0.360046166876 | 0.00051498895134 | [u'leuA'] | 0.0 | 0.0 | nan | |
G1PACT | False | False | 0.0587682773023 | 8.40587021452e-05 | [u'glmU'] | 0.0 | 0.0 | nan | |
CS | True | False | 8.16163711651 | 0.011673927753 | [u'gltA'] | 0.0 | 1.0 | -2.71754690503 | |
ACGS | False | False | 0.269294840319 | 0.000385183568598 | [u'argA'] | 0.0 | 0.0 | nan | |
ACCOAC | False | False | 0.0268452661692 | 3.83978965611e-05 | [u'accB', u'accC', u'accD', u'accA'] | 0.0 | 0.0 | nan | |
ACACT8r_reverse | True | False | 0.0436554083775 | 6.24421395058e-05 | [u'fadA', u'fadI'] | 0.0 | 2.0 | -9.68211959615 | |
ACACT7r | True | False | 0.22011410477 | 0.000314838324691 | [u'fadA', u'fadI'] | 0.0 | 2.0 | -9.68211959615 | |
ACACT6r | True | False | 0.227319093089 | 0.000325143918028 | [u'fadA', u'fadI'] | 0.0 | 2.0 | -9.68211959615 | |
ACACT5r | True | False | 0.260525120226 | 0.000372639874566 | [u'fadA', u'fadI'] | 0.0 | 2.0 | -9.68211959615 | |
ACACT4r | True | False | 0.260632800456 | 0.000372793894061 | [u'fadA', u'fadI'] | 0.0 | 2.0 | -9.68211959615 | |
ACACT3r | True | False | 0.261014703832 | 0.000373340146285 | [u'fadA', u'fadI'] | 0.0 | 2.0 | -9.68211959615 | |
ACACT2r | True | False | 0.260140440566 | 0.000372089651309 | [u'fadA', u'fadI'] | 0.0 | 2.0 | -9.68211959615 | |
ACACT1r | True | False | 0.261028049571 | 0.000373359235248 | [u'fadA', u'fadI', u'atoB'] | 0.0 | 2.0 | -9.68211959615 |
df = metabolite_panel_anaerobic_101['pep_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | ENO | False | False | 18.9459969929 | 0.0468157518118 | [u'eno'] | 0.0 | 0.0 | nan |
consuming | PYK | True | True | 0.0975618664448 | 0.000241076367081 | [u'pykF', u'pykA'] | 1.0 | 1.0 | 3.6770040631 |
PSCVT | False | False | 0.0929107613053 | 0.000229583438842 | [u'aroA'] | 0.0 | 0.0 | nan | |
PPC | False | False | 0.7865560074 | 0.00194358791688 | [u'ppc'] | 0.0 | 0.0 | nan | |
GLCptspp | True | True | 10.0 | 0.0247101019964 | [u'ptsG', u'manX', u'crr', u'ptsH', u'manY', u'manZ', u'ptsI', u'malX'] | 1.0 | 1.0 | 1.14780003733 | |
DHAPT | True | True | 7.86463461894 | 0.0194335923599 | [u'dhaL', u'dhaK', u'ptsI', u'ptsH', u'dhaM'] | 2.0 | 2.0 | 3.43769754423 | |
DDPA | False | False | 0.0900787310708 | 0.000222585463247 | [u'aroH', u'aroG', u'aroF'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['pep_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | ENO | True | True | 15.944946885 | 0.0228067182238 | [u'eno'] | 1.0 | 1.0 | -0.708758217081 |
consuming | UAGCVT | False | False | 0.0226804296787 | 3.24407583548e-05 | [u'murA'] | 0.0 | 0.0 | nan |
PYK | True | True | 0.20591111489 | 0.000294523199751 | [u'pykF', u'pykA'] | 1.0 | 1.0 | 1.62575576097 | |
PSCVT | False | False | 0.30964064659 | 0.000442891847073 | [u'aroA'] | 0.0 | 0.0 | nan | |
PPC | False | False | 2.40574986509 | 0.00344104371658 | [u'ppc'] | 0.0 | 0.0 | nan | |
KDOPS | False | False | 0.0201111269148 | 2.87657781499e-05 | [u'kdsA'] | 0.0 | 0.0 | nan | |
GLCptspp | True | True | 10.0 | 0.0143034143596 | [u'ptsG', u'manX', u'crr', u'ptsH', u'manY', u'manZ', u'ptsI', u'malX'] | 1.0 | 2.0 | 1.35151438926 | |
DHAPT | False | False | 2.66943102851 | 0.0038181978105 | [u'dhaL', u'dhaK', u'ptsI', u'ptsH', u'dhaM'] | 0.0 | 0.0 | nan | |
DDPA | False | False | 0.305885198821 | 0.000437520274519 | [u'aroH', u'aroG', u'aroF'] | 0.0 | 0.0 | nan |
df = metabolite_panel_anaerobic_101['succoa_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | SUCOAS | True | False | 0.119108219478 | 0.000294317625192 | [u'sucD', u'sucC'] | 0.0 | 2.0 | -9.11368614951 |
consuming | THDPS | False | False | 0.0874390302466 | 0.000216062735586 | [u'dapD'] | 0.0 | 0.0 | nan |
HSST | False | False | 0.0378565407447 | 9.35438983034e-05 | [u'metA'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['succoa_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | AKGDH | True | False | 7.26670224929 | 0.0103938653299 | [u'sucA', u'lpd', u'sucB'] | 0.0 | 3.0 | -7.29009006112 |
consuming | THDPS | False | False | 0.296921424549 | 0.000424699016755 | [u'dapD'] | 0.0 | 0.0 | nan |
SUCOAS_reverse | True | False | 6.84727218826 | 0.00979393713413 | [u'sucD', u'sucC'] | 0.0 | 2.0 | -5.36626496942 | |
HSST | False | False | 0.128551494395 | 0.000183872529087 | [u'metA'] | 0.0 | 0.0 | nan |
df = metabolite_panel_anaerobic_101['ac_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | CYSS | False | False | 0.0600301245583 | 0.00014833505007 | [u'cysK', u'cysM'] | 0.0 | 0.0 | nan |
ACODA | False | False | 0.0793034040046 | 0.000195959520162 | [u'argE'] | 0.0 | 0.0 | nan | |
ACKr_reverse | True | False | 8.09784901725 | 0.0200098675168 | [u'purT', u'tdcD', u'ackA'] | 0.0 | 1.0 | 1.14701779971 | |
consuming | ACKr | True | False | 0.0121256687998 | 2.99626512819e-05 | [u'purT', u'tdcD', u'ackA'] | 0.0 | 1.0 | 1.14701779971 |
df = metabolite_panel_nitrate_101['ac_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | UHGADA | False | False | 0.0134074179432 | 1.91771854333e-05 | [u'lpxC'] | 0.0 | 0.0 | nan |
CYSS | False | False | 0.203847527247 | 0.000291571564838 | [u'cysK', u'cysM'] | 0.0 | 0.0 | nan | |
ACODA | False | False | 0.269294840319 | 0.000385183568598 | [u'argE'] | 0.0 | 0.0 | nan | |
ACKr_reverse | True | False | 0.0190724427628 | 2.72801051686e-05 | [u'purT', u'tdcD', u'ackA'] | 0.0 | 1.0 | 0.77094280346 | |
consuming | ACS | True | True | 0.0607009136363 | 8.68230319743e-05 | [u'acs'] | 1.0 | 1.0 | -5.52079862311 |
ACKr | True | False | 0.444921314634 | 0.000636389392061 | [u'purT', u'tdcD', u'ackA'] | 0.0 | 1.0 | 0.77094280346 |
df = metabolite_panel_anaerobic_101['for_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | PFL | True | False | 17.2725055582 | 0.0426805374078 | [u'pflA', u'pflB', u'tdcE', u'pflD', u'yfiD', u'pflC'] | 0.0 | 2.0 | 4.05181918871 |
consuming | GART | False | False | 0.0261712536521 | 6.46694347119e-05 | [u'purT'] | 0.0 | 0.0 | nan |
FORtppi | True | False | 17.2452785422 | 0.0426132591735 | [u'focA', u'focB'] | 0.0 | 1.0 | 0.664456635363 |
df = metabolite_panel_nitrate_101['for_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
MultiIndex [] | Empty DataFrame |
df = metabolite_panel_anaerobic_101['etoh_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | ALCD2x_reverse | True | False | 8.0873620921 | 0.0199839542178 | [u'adhP', u'adhE', u'frmA'] | 0.0 | 1.0 | 0.587546853664 |
df = metabolite_panel_nitrate_101['etoh_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
MultiIndex [] | Empty DataFrame |
df = metabolite_panel_anaerobic_101['13dpg_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | GAPD | True | True | 19.3290467436 | 0.0477622716529 | [u'gapA'] | 1.0 | 1.0 | 0.225939104089 |
consuming | PGK_reverse | False | False | 19.3293313682 | 0.0477629749633 | [u'pgk'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['13dpg_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | GAPD | True | True | 17.2938829399 | 0.0247361573575 | [u'gapA'] | 1.0 | 1.0 | -0.139548915179 |
consuming | PGK_reverse | False | False | 17.2915724382 | 0.0247328525512 | [u'pgk'] | 0.0 | 0.0 | nan |
df = metabolite_panel_anaerobic_101['3pg_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | PGK_reverse | False | False | 19.3293313682 | 0.0477629749633 | [u'pgk'] | 0.0 | 0.0 | nan |
consuming | PGM_reverse | True | True | 18.9442613729 | 0.0468114630771 | [u'ytjC', u'gpmM', u'gpmA'] | 1.0 | 1.0 | 1.10779700174 |
PGCD | False | False | 0.383889615491 | 0.000948595155415 | [u'serA'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['13dpg_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | GAPD | True | True | 17.2938829399 | 0.0247361573575 | [u'gapA'] | 1.0 | 1.0 | -0.139548915179 |
consuming | PGK_reverse | False | False | 17.2915724382 | 0.0247328525512 | [u'pgk'] | 0.0 | 0.0 | nan |
df = metabolite_panel_anaerobic_101['oaa_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | PPC | False | False | 0.7865560074 | 0.00194358791688 | [u'ppc'] | 0.0 | 0.0 | nan |
MDH | True | False | 0.170285349565 | 0.000420776835624 | [u'mdh'] | 0.0 | 1.0 | -3.82955472585 | |
consuming | CS | True | False | 0.263545269736 | 0.000651223049586 | [u'gltA'] | 0.0 | 1.0 | -3.39561619493 |
ASPTA_reverse | False | False | 0.696537990833 | 0.00172115247979 | [u'aspC'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['oaa_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | PPC | False | False | 2.40574986509 | 0.00344104371658 | [u'ppc'] | 0.0 | 0.0 | nan |
MDH | True | False | 8.10514229615 | 0.0115931208705 | [u'mdh'] | 0.0 | 1.0 | -1.73539482182 | |
consuming | CS | True | False | 8.16163711651 | 0.011673927753 | [u'gltA'] | 0.0 | 1.0 | -2.71754690503 |
ASPTA_reverse | False | False | 2.35397083122 | 0.00336698201892 | [u'aspC'] | 0.0 | 0.0 | nan |
df = metabolite_panel_anaerobic_101['lac__D_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
MultiIndex [] | Empty DataFrame |
df = metabolite_panel_nitrate_101['lac__D_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
MultiIndex [] | Empty DataFrame |
df = metabolite_panel_anaerobic_101['h2_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
MultiIndex [] | Empty DataFrame |
df = metabolite_panel_nitrate_101['h2_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
MultiIndex [] | Empty DataFrame |
df = metabolite_panel_anaerobic_101['glyc3p_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | G3PD2_reverse | False | False | 0.0414638909066 | 0.000102457697347 | [u'gpsA'] | 0.0 | 0.0 | nan |
consuming | G3PAT161 | False | False | 0.0113099566944 | 2.79470183495e-05 | [u'plsB', u'acpP'] | 0.0 | 0.0 | nan |
G3PAT160 | False | False | 0.0146148040673 | 3.6113329916e-05 | [u'plsB', u'acpP'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['glyc3p_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | G3PD2_reverse | False | False | 0.136812803847 | 0.000195689022311 | [u'gpsA'] | 0.0 | 0.0 | nan |
consuming | PGSA161 | False | False | 0.0105469713964 | 1.50857702121e-05 | [u'pgsA'] | 0.0 | 0.0 | nan |
PGSA160 | False | False | 0.0135595693554 | 1.93948139028e-05 | [u'pgsA'] | 0.0 | 0.0 | nan | |
G3PAT181 | True | True | 0.0199187787291 | 2.84906545698e-05 | [u'plsB', u'acpP'] | 1.0 | 1.0 | 0.248539214466 | |
G3PAT161 | True | True | 0.0386235022895 | 5.52447957263e-05 | [u'plsB', u'acpP'] | 1.0 | 1.0 | 0.248539214466 | |
G3PAT160 | True | True | 0.0497569903393 | 7.11694850107e-05 | [u'plsB', u'acpP'] | 1.0 | 1.0 | 0.248539214466 |
df = metabolite_panel_anaerobic_101['g6p_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | GLCptspp | True | True | 10.0 | 0.0247101019964 | [u'ptsG', u'manX', u'crr', u'ptsH', u'manY', u'manZ', u'ptsI', u'malX'] | 1.0 | 1.0 | 1.14780003733 |
consuming | PGMT_reverse | False | False | 0.0494918698179 | 0.00012229491512 | [u'yqaB', u'pgm'] | 0.0 | 0.0 | nan |
PGI | False | False | 9.95606096886 | 0.0246015282023 | [u'pgi'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['g6p_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | GLCptspp | True | True | 10.0 | 0.0143034143596 | [u'ptsG', u'manX', u'crr', u'ptsH', u'manY', u'manZ', u'ptsI', u'malX'] | 1.0 | 2.0 | 1.35151438926 |
consuming | PGMT_reverse | False | False | 0.164177504829 | 0.000234829888009 | [u'yqaB', u'pgm'] | 0.0 | 0.0 | nan |
PGI | False | False | 8.5779465697 | 0.0122693924141 | [u'pgi'] | 0.0 | 0.0 | nan | |
G6PDH2r | False | False | 1.27234596105 | 0.00181988914897 | [u'zwf'] | 0.0 | 0.0 | nan |
df = metabolite_panel_anaerobic_101['f6p_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | PGI | False | False | 9.95606096886 | 0.0246015282023 | [u'pgi'] | 0.0 | 0.0 | nan |
consuming | TKT2_reverse | False | False | 0.14421789557 | 0.000356363890924 | [u'tktB', u'tktA'] | 0.0 | 0.0 | nan |
TALA_reverse | False | False | 0.139259584127 | 0.000344111852776 | [u'talB', u'talA'] | 0.0 | 0.0 | nan | |
PFK | False | False | 1.79272979129 | 0.00442985359948 | [u'pfkA', u'pfkB'] | 0.0 | 0.0 | nan | |
GF6PTA | False | False | 0.0173064007943 | 4.27642928819e-05 | [u'glmS'] | 0.0 | 0.0 | nan | |
F6PA | False | False | 7.86689298566 | 0.0194391728071 | [u'fsaB', u'fsaA'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['f6p_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | TALA | False | False | 0.0151481520909 | 2.16670296138e-05 | [u'talB', u'talA'] | 0.0 | 0.0 | nan |
PGI | False | False | 8.5779465697 | 0.0122693924141 | [u'pgi'] | 0.0 | 0.0 | nan | |
consuming | TKT2_reverse | False | False | 0.0616290585778 | 8.81505961427e-05 | [u'tktB', u'tktA'] | 0.0 | 0.0 | nan |
TALA_reverse | False | False | 0.179351050481 | 0.000256533239086 | [u'talB', u'talA'] | 0.0 | 0.0 | nan | |
PFK | False | False | 5.62193955837 | 0.00804129310078 | [u'pfkA', u'pfkB'] | 0.0 | 0.0 | nan | |
GF6PTA | False | False | 0.0587682773023 | 8.40587021451e-05 | [u'glmS'] | 0.0 | 0.0 | nan | |
F6PA | True | True | 2.67476083014 | 0.00382582124662 | [u'fsaB', u'fsaA'] | 1.0 | 1.0 | 0.349968647141 |
df = metabolite_panel_anaerobic_101['r5p_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | TKT1_reverse | False | False | 0.0456504885766 | 0.000112802822892 | [u'tktB', u'tktA'] | 0.0 | 0.0 | nan |
RPI_reverse | False | False | 0.180999192376 | 0.000447250850489 | [u'rpiA', u'rpiB'] | 0.0 | 0.0 | nan | |
consuming | PRPPS | False | False | 0.199598304985 | 0.00049320944745 | [u'prs'] | 0.0 | 0.0 | nan |
PPM_reverse | False | False | 0.0323938026784 | 8.00454168235e-05 | [u'deoB', u'yhfW'] | 0.0 | 0.0 | nan |
df = metabolite_panel_nitrate_101['r5p_c']
HTML(df[df['flux'].apply(float32) > .01].dropna().sort(ascending=False).to_html())
flux | percent_total | genes | novel_regulation | total_regulation | direction | ||||
---|---|---|---|---|---|---|---|---|---|
producing | RPI_reverse | False | False | 1.03399290281 | 0.00147896289338 | [u'rpiA', u'rpiB'] | 0.0 | 0.0 | nan |
PRPPS_reverse | False | False | 0.0152695717711 | 2.18407012134e-05 | [u'prs'] | 0.0 | 0.0 | nan | |
consuming | TKT1 | False | False | 0.280092326935 | 0.000400627661108 | [u'tktB', u'tktA'] | 0.0 | 0.0 | nan |
PRPPS | False | False | 0.714815145596 | 0.00102242972179 | [u'prs'] | 0.0 | 0.0 | nan | |
PPM_reverse | False | False | 0.0585293809752 | 8.37169988296e-05 | [u'deoB', u'yhfW'] | 0.0 | 0.0 | nan |