Notebook

ArcA expression data comparison for Fig. S6¶

In [88]:

from trnlib.omeORM import *
from pandas import *

from numpy import array
from sqlalchemy import func

from IPython.core.display import HTML

ome = Session()

In [12]:

s12 = read_table('S12_delta_arcA.txt', index_col='b number')

In [11]:

HTML(s12.to_html())

Out[11]:

	Strand	Operon	WT	ΔarcA	Fold change	P value
b number
b0721	forward	sdhCDAB-sucABCD	7.4	14.4	133.5	5.450000e-07
b0432	reverse	cyoABCDE	7.5	13.5	64.9	5.550000e-07
b4069	reverse	acs-yjcH-actP	6.1	12.0	57.5	2.170000e-07
b1415	forward	aldA	7.8	13.0	36.1	9.620000e-08
b2210	reverse	mqo	6.1	11.1	31.8	7.290000e-08
b1014	reverse	putA	5.9	10.8	30.8	1.210000e-07
b2150	reverse	mglBAC	5.5	10.3	29.2	1.110000e-07
b3846	reverse	fadBA	6.3	11.0	27.2	3.040000e-07
b1612	reverse	fumA	8.2	12.9	26.0	2.030000e-07
b1020	forward	phoH	5.5	10.2	25.3	2.280000e-07
b0346	reverse	mhpR-lacI	6.2	10.8	23.9	1.430000e-05
b2310	reverse	argT-hisJQMP	6.5	11.0	22.6	2.280000e-07
b0598	forward	cstA	7.3	11.7	21.5	7.110000e-06
b0124	reverse	gcd	6.8	11.1	20.0	2.270000e-07
b3962	reverse	sthA	7.5	11.7	18.3	1.730000e-06
b0221	reverse	fadE	6.3	10.5	17.5	4.600000e-07
b1189	forward	dadAX	8.7	12.7	16.0	3.100000e-06
b1422	reverse	ydcI	7.0	11.0	15.9	3.730000e-07
b3820	reverse	yigI	6.2	10.1	15.6	5.480000e-07
b1297	reverse	puuA	6.8	10.7	15.3	2.740000e-07
b3528	reverse	dctA	7.5	11.5	15.3	5.750000e-07
b0118	forward	acnB	9.6	13.3	13.7	1.110000e-06
b2181	reverse	yejG	7.4	10.9	11.9	5.570000e-07
b1778	reverse	msrB	9.2	12.7	11.6	2.260000e-07
b1777	reverse	yeaC	8.0	11.5	11.1	8.080000e-07
b1748	reverse	astCADBE	5.5	8.9	10.6	5.510000e-07
b1298	forward	puuDR	7.4	10.8	10.6	5.540000e-07
b2342	reverse	fadIJ	5.5	8.8	10.2	5.460000e-07
b2980	forward	glcC	5.7	9.0	9.8	3.420000e-07
b1276	forward	acnA	7.8	11.0	9.2	1.550000e-06
b0450	forward	glnK-amtB	5.2	8.3	8.8	3.250000e-03
b2587	reverse	kgtP	11.0	14.2	8.8	3.620000e-07
b3236	reverse	mdh	10.3	13.5	8.8	1.510000e-05
b2586	forward	yfiM	7.1	10.2	8.6	1.280000e-06
b1611	reverse	fumC	6.4	9.5	8.4	2.190000e-06
b3605	forward	lldPRD	6.6	9.6	8.3	2.730000e-06
b2518	reverse	ndk	9.2	12.3	8.2	4.710000e-06
b3453	reverse	ugpBAECQ	6.3	9.3	8.2	2.950000e-06
b0458	reverse	ylaC	6.1	9.1	7.7	5.910000e-05
b4376	forward	osmY	9.5	12.4	7.5	3.650000e-06
b2979	reverse	glcDEFGBA	6.4	9.2	7.1	6.940000e-07
b0720	reverse	gltA	12.3	15.1	7.1	9.660000e-06
b2537	reverse	hcaR	6.8	9.6	6.8	1.090000e-06
b0453	forward	ybaY	7.3	10.0	6.4	1.140000e-04
b1300	forward	puuCBE	7.6	10.3	6.4	3.370000e-05
b0116	forward	lpdA	11.9	14.5	6.1	1.100000e-06
b3894	reverse	fdoGHI-fdhE	6.6	9.2	6.0	8.850000e-06
b0314	forward	betT	5.9	8.5	5.9	4.670000e-05
b3160	forward	yhbW	7.7	10.2	5.7	5.560000e-06
b3073	forward	ygjG	7.8	10.3	5.5	4.750000e-05
b2111	reverse	yehDCBA	6.5	8.9	5.4	3.120000e-05
b0240	forward	crl	9.8	12.2	5.2	5.870000e-05
b2155	reverse	cirA	6.5	8.9	5.2	1.250000e-03
b2463	reverse	maeB	8.3	10.6	4.9	1.600000e-05
b4568	forward	ytjA	8.5	10.7	4.7	8.020000e-04
b1163	reverse	ycgF	6.0	8.2	4.6	5.530000e-05
b4519	forward	icdC	7.3	9.4	4.4	2.060000e-04
b0313	reverse	betIBA	6.0	8.1	4.4	5.200000e-04
b3819	reverse	rarD	6.6	8.7	4.1	1.500000e-05
b3128	forward	garD	8.0	10.0	4.0	3.940000e-05
b1136	forward	icdA	13.0	14.9	4.0	2.870000e-04
b0882	forward	clpA	10.6	12.5	3.7	3.910000e-05
b4034	reverse	malEFG	8.7	10.5	3.4	5.400000e-04
b1296	reverse	puuP	6.2	7.9	3.4	3.370000e-05
b1332	forward	ynaJ	9.0	10.7	3.4	4.410000e-04
b1256	forward	ompW	8.1	9.8	3.3	5.520000e-03
b3523	forward	yhjE	10.5	12.2	3.2	4.420000e-04
b1805	reverse	fadD-sroD	7.0	8.7	3.2	1.450000e-04
b0383	forward	phoA-psiF	7.7	9.4	3.2	2.930000e-03
b0836	forward	bssR	10.7	12.3	3.2	9.960000e-04
b0113	forward	pdhR-aceEF-lpd	8.3	9.9	3.2	2.120000e-02
b2677	forward	proVWX	5.8	7.4	3.1	6.730000e-04
b2172	forward	yeiQ	6.1	7.8	3.1	2.050000e-04
b2844	reverse	yqeF	6.0	7.6	3.1	5.860000e-04
b3081	forward	fadH	6.6	8.2	3.1	1.280000e-03
b4490	NaN	NaN	5.9	7.5	3.1	2.500000e-02
b1040	reverse	csgDEFG	8.0	9.6	3.0	4.430000e-04
b0330	reverse	prpR	6.1	7.6	2.9	1.400000e-03
b4340	reverse	yjiR	6.7	8.2	2.9	2.110000e-04
b0031	forward	dapB	9.9	11.5	2.9	7.410000e-05
b3942	forward	katG	12.6	14.1	2.9	1.450000e-04
b0755	reverse	gpmA	11.1	12.6	2.9	7.440000e-05
b2344	forward	fadL	7.3	8.8	2.8	7.220000e-05
b3351	reverse	kefGB-yheV	6.9	8.4	2.8	3.830000e-05
b3995	reverse	rsd	8.4	10.0	2.8	1.300000e-04
b0655	reverse	gltI-sroC-gltJKL	10.2	11.7	2.8	9.180000e-05
b4014	forward	aceBAK	13.1	14.6	2.8	9.940000e-05
b3403	forward	pck	10.4	11.9	2.8	1.010000e-04
b1021	reverse	pgaABCD	6.3	7.8	2.7	4.970000e-04
b0584	reverse	fepA-entD	6.4	7.8	2.7	4.120000e-03
b2287	reverse	nuoABCEFGHIJKLMN	11.8	13.3	2.7	8.390000e-04
b1674	reverse	ydhYVWXUT	8.4	9.9	2.7	1.290000e-02
b0628	reverse	lipA	11.0	12.4	2.7	9.560000e-04
b2582	forward	trxC	6.7	8.1	2.7	4.050000e-03
b1452	forward	yncE	7.0	8.4	2.6	2.910000e-02
b4035	forward	malK-lamB-malM	6.4	7.8	2.6	8.780000e-04
b0306	forward	ykgEFG	6.7	8.0	2.6	8.330000e-03
b1534	forward	ydeE	6.6	8.0	2.6	3.280000e-04
b3397	reverse	nudE	6.5	7.9	2.6	1.700000e-04
b0854	forward	potFGHI	11.3	12.6	2.6	5.760000e-05
b2574	forward	nadB	10.6	12.0	2.6	1.690000e-03
b2152	reverse	folE-yeiB	7.9	9.2	2.5	2.120000e-04
b3751	forward	rbsDACBKR	9.8	11.2	2.5	3.370000e-04
b1451	reverse	yncD	6.8	8.1	2.5	6.000000e-04
b0821	reverse	ybiU	5.9	7.2	2.4	1.440000e-04
b4512	forward	ybdD	7.2	8.4	2.4	9.910000e-03
b2392	reverse	mntH	8.3	9.6	2.4	2.410000e-02
b0608	forward	ybdR	8.6	9.9	2.4	7.830000e-03
b1164	forward	ycgZ-ymgA-ariR-ymgC	5.6	6.9	2.4	4.880000e-04
b3795	forward	yifK	10.1	11.3	2.4	1.330000e-04
b1015	forward	putP	9.9	11.1	2.4	4.930000e-04
b3268	forward	yhdWXYZ	6.7	7.9	2.3	3.470000e-04
b1702	reverse	ppsA	9.1	10.3	2.3	2.750000e-04
b3324	forward	gspCDEFGHIJKLMO	6.6	7.8	2.3	9.880000e-04
b1444	forward	ydcW	7.9	9.2	2.3	2.430000e-04
b0452	reverse	tesB	8.5	9.7	2.3	7.600000e-03
b4139	reverse	aspA	9.2	10.4	2.3	3.260000e-04
b1765	reverse	ydjA-selD-topB	11.2	12.3	2.2	2.270000e-04
b0593	forward	entCEBAH	6.5	7.7	2.2	1.660000e-02
b3592	reverse	yibF	7.5	8.7	2.2	5.940000e-04
b1536	reverse	ydeI	7.2	8.4	2.2	1.500000e-03
b2209	forward	eco	9.0	10.2	2.2	1.500000e-03
b0527	reverse	ybcI	8.2	9.3	2.2	2.060000e-02
b0382	forward	iraP	9.8	11.0	2.2	1.860000e-03
b3744	forward	asnA	8.1	9.2	2.2	7.070000e-04
b3616	reverse	kbl-tdh	9.4	10.5	2.1	9.870000e-04
b1384	reverse	feaR	5.9	7.0	2.1	2.380000e-04
b0319	forward	yahDEFG	5.7	6.8	2.1	3.360000e-02
b0304	reverse	ykgC	8.3	9.4	2.1	6.980000e-03
b3662	reverse	nepI	7.0	8.1	2.1	2.880000e-03
b0443	forward	fadM	6.8	7.9	2.1	3.820000e-02
b1761	forward	gdhA	13.4	14.5	2.1	8.070000e-04
b0286	reverse	yagTSRQ	5.7	6.8	2.1	1.250000e-02
b0356	reverse	frmRAB	9.4	10.4	2.1	4.820000e-02
b1607	reverse	ydgC	7.9	8.9	2.0	2.040000e-02
b1533	reverse	eamA	9.7	10.7	2.0	2.070000e-04
b1197	reverse	treA	10.2	11.2	2.0	9.770000e-04
b2876	reverse	yqeC	6.4	7.4	2.0	8.070000e-04
b2133	forward	dld	10.4	11.4	2.0	2.830000e-03
b0020	forward	nhaAR	8.1	7.1	-2.0	8.410000e-04
b4280	forward	yjhBC	9.2	8.2	-2.0	8.200000e-04
b1826	reverse	mgrB	10.8	9.8	-2.0	4.110000e-03
b1223	forward	narK	10.8	9.8	-2.0	1.520000e-03
b2690	reverse	yqaBA	10.1	9.1	-2.0	4.430000e-04
b1251	reverse	yciI	10.2	9.2	-2.0	7.800000e-03
b2419	forward	yfeKS	7.2	6.2	-2.0	4.410000e-04
b1623	forward	add	9.3	8.2	-2.0	2.970000e-03
b3042	forward	yqiC	10.8	9.8	-2.0	9.210000e-04
b4598	reverse	yncL	10.8	9.7	-2.0	1.110000e-02
b0034	forward	caiF	11.2	10.2	-2.0	9.180000e-04
b2350	forward	yfdGHI	12.4	11.3	-2.1	1.850000e-03
b1243	forward	oppABCDF	15.2	14.2	-2.1	1.570000e-04
b4057	forward	yjbQR	10.4	9.3	-2.1	4.440000e-04
b0211	reverse	mltD	10.0	9.0	-2.1	3.720000e-03
b0189	reverse	yaeP-rof	7.8	6.7	-2.1	3.720000e-03
b3103	forward	yhaH	9.5	8.5	-2.1	2.760000e-03
b2346	forward	mlaA	9.5	8.4	-2.1	6.180000e-03
b3865	reverse	yihA	8.1	7.1	-2.1	1.290000e-03
b2617	forward	smpA	8.5	7.4	-2.1	1.010000e-02
b3028	forward	mdaB	9.5	8.4	-2.1	6.690000e-04
b2351	forward	yfdGHI	12.4	11.3	-2.1	4.450000e-04
b1874	reverse	cutC	8.5	7.4	-2.2	3.420000e-04
b3466	forward	rsmD-yhhL	7.5	6.4	-2.2	6.990000e-03
b3343	reverse	yheONML	8.0	6.8	-2.2	9.770000e-03
b3023	reverse	ygiV	8.4	7.3	-2.2	1.130000e-03
b2175	forward	spr	9.1	8.0	-2.2	5.590000e-03
b3494	reverse	uspB	9.6	8.4	-2.2	1.030000e-03
b1792	forward	yeaO	9.2	8.1	-2.2	3.870000e-04
b0075	reverse	leuLABCD	9.7	8.6	-2.2	8.990000e-03
b4117	reverse	adiA	7.1	6.0	-2.2	5.510000e-04
b1869	forward	yecN-cmoAB	10.0	8.8	-2.2	9.230000e-04
b0961	reverse	yccFS	11.4	10.3	-2.2	3.250000e-04
b4595	forward	yciY	7.8	6.6	-2.2	4.150000e-03
b1250	reverse	kch	9.3	8.1	-2.3	4.430000e-04
b2796	forward	sdaCB	8.5	7.2	-2.3	4.720000e-04
b4640	reverse	upp-uraA	8.0	6.8	-2.3	5.030000e-03
b1626	forward	ydgK-rsxABCDGE-nth	9.6	8.3	-2.3	2.260000e-04
b1825	reverse	yebO	8.3	7.1	-2.3	5.760000e-04
b1273	reverse	yciN	9.6	8.3	-2.4	1.730000e-04
b4606	reverse	ypfM	7.0	5.8	-2.4	1.110000e-02
b0485	forward	ybaST	12.0	10.8	-2.4	2.440000e-03
b1224	forward	narGHJI	11.6	10.3	-2.4	8.080000e-04
b1000	reverse	cbpAM	12.3	11.0	-2.4	5.680000e-04
b0704	forward	ybfOC	7.3	6.0	-2.4	4.690000e-04
b0762	forward	ybhT	8.4	7.1	-2.5	1.140000e-03
b1054	reverse	lpxL	10.4	9.1	-2.5	5.850000e-05
b0001	forward	thrLABC	12.7	11.4	-2.5	6.510000e-04
b0968	forward	yccX	7.9	6.6	-2.5	3.860000e-04
b1143	forward	ymfI	9.5	8.2	-2.5	1.820000e-03
b4046	reverse	zur	8.5	7.2	-2.5	6.490000e-04
b1634	forward	tppB	9.1	7.8	-2.5	6.140000e-04
b4402	NaN	yjjY	13.2	11.8	-2.6	3.650000e-04
b1974	forward	yodB	8.9	7.5	-2.6	2.240000e-03
b0833	forward	yliEF	7.8	6.4	-2.6	3.300000e-04
b0559	reverse	ybcW	7.0	5.6	-2.6	2.460000e-04
b1185	reverse	dsbB	8.3	6.9	-2.7	1.280000e-02
b4641	NaN	NaN	8.3	6.9	-2.7	4.590000e-03
b4377	forward	yjjUV	10.4	8.9	-2.8	1.270000e-04
b4589	reverse	ylcI	8.8	7.3	-2.8	5.370000e-03
b0622	forward	pagP	7.8	6.3	-2.8	9.290000e-03
b3510	reverse	hdeAB-yhiD	15.0	13.4	-2.9	1.530000e-03
b1073	forward	flgBCDEFGHIJ	7.3	5.8	-2.9	1.650000e-02
b2290	forward	yfbQ	10.8	9.2	-2.9	3.580000e-05
b4187	forward	aidB	10.4	8.8	-3.0	1.180000e-03
b3071	forward	yqjI	10.0	8.4	-3.0	5.830000e-05
b4077	forward	gltP	9.2	7.6	-3.0	1.740000e-04
b3516	reverse	gadXW	11.3	9.6	-3.1	1.910000e-04
b0699	forward	ybfA	7.3	5.7	-3.2	8.610000e-04
b1923	reverse	fliC	8.3	6.5	-3.6	1.000000e-02
b0972	forward	hyaABCDEF	14.0	12.1	-3.7	1.750000e-04
b3408	forward	feoABC	9.4	7.5	-3.7	6.000000e-03
b2847	forward	yqeIJ	8.5	6.6	-3.8	3.370000e-05
b3506	forward	slp-dctR	12.7	10.7	-4.0	1.360000e-03
b4409	forward	blr	9.9	7.9	-4.1	8.640000e-04
b0621	reverse	dcuC	9.2	7.1	-4.1	4.680000e-04
b0978	forward	appCB-yccB-appA	12.5	10.4	-4.1	1.070000e-03
b3511	forward	hdeD	14.7	12.7	-4.2	4.160000e-04
b1493	reverse	gadBC	13.3	11.2	-4.2	3.710000e-03
b0564	forward	appY	8.8	6.5	-4.6	2.930000e-05
b3517	reverse	gadAXW	12.9	10.7	-4.8	1.700000e-03
b2669	reverse	stpA	11.1	8.7	-5.2	3.050000e-05
b1172	reverse	ymgGD	10.0	7.6	-5.4	4.590000e-05
b4354	reverse	yjiY	8.6	6.0	-6.2	1.130000e-04
b1625	forward	cnu	10.1	7.5	-6.4	1.060000e-05
b0848	forward	ybjM	8.9	6.2	-6.4	5.430000e-06
b4116	reverse	adiY	10.4	7.6	-6.9	1.930000e-05
b4115	reverse	adiC	9.3	6.3	-8.0	4.790000e-05
b3512	forward	gadE-mdtEF	12.4	8.8	-11.4	2.440000e-04
b3491	forward	yhiM	10.2	6.3	-15.0	8.150000e-06

In [6]:

aa = AllAnalysis
ome.query(aa).filter(and_(or_(aa.target1 == 'delta-arcA', aa.target2 == 'delta-arcA'),\
                          or_(aa.target1 == 'wt', aa.target2 == 'wt'), aa.bnum == 'b1611',\
                          aa.eacceptor1 == 'anaerobic')).all()

Out[6]:

[]

In [79]:

aa = AllAnalysis
ome.query(aa).filter(and_(or_(aa.target1 == 'delta-arcA', aa.target2 == 'delta-arcA'),\
                          or_(aa.target1 == 'wt', aa.target2 == 'wt'), aa.fdr < .05, aa.gene_name.ilike('yfb%'),\
                          or_(and_(aa.eacceptor1 == 'anaerobic', aa.eacceptor2 == 'anaerobic'),\
                              and_(aa.eacceptor1 == 'NO3', aa.eacceptor2 == 'NO3'),\
                              and_(aa.eacceptor1 == 'O2', aa.eacceptor2 == 'O2')))).all()

Out[79]:

[AllAnalysis (fdr: 0.035516, fold change -0.233333): for Gene: yfbT/G7187 (b2293) Strain: delta-arcA-->wt on Condition: C:glucose, N:NH4Cl, e:anaerobic,
 AllAnalysis (fdr: 0.000185, fold change -1.255000): for Gene: yfbV/G7189 (b2295) Strain: delta-arcA-->wt on Condition: C:glucose, N:NH4Cl, e:anaerobic,
 AllAnalysis (fdr: 0.010148, fold change 0.716667): for Gene: yfbM/G7179 (b2272) Strain: wt-->delta-arcA on Condition: C:glucose, N:NH4Cl, e:NO3,
 AllAnalysis (fdr: 0.023336, fold change 0.906667): for Gene: yfbS/G7186 (b2292) Strain: wt-->delta-arcA on Condition: C:glucose, N:NH4Cl, e:NO3,
 AllAnalysis (fdr: 0.041744, fold change 0.236667): for Gene: yfbT/G7187 (b2293) Strain: wt-->delta-arcA on Condition: C:glucose, N:NH4Cl, e:NO3,
 AllAnalysis (fdr: 0.023259, fold change -0.320000): for Gene: yfbU/G7188 (b2294) Strain: wt-->delta-arcA on Condition: C:glucose, N:NH4Cl, e:NO3]

In [47]:

array([x.value for x in ome.query(ExpressionData).filter_by(bnum='b3327').all()]).mean()

Out[47]:

2.2298529411764716

In [82]:

unmapped = {
                'b4139':{'tu':'aspA', 'mistake':True, 'reason': 'dcuA is diff expressed in same operon'},\
                'b0356':{'tu':'frmRAB', 'mistake':True, 'reason': 'have frmB under nitrate'},\
                'b1223':{'tu':'narK', 'mistake':False, 'reason': 'have narX nearby but not narK or narG'},\
                'b3042':{'tu':'yqiC', 'mistake':False, 'reason': 'have yqiAB but not on same operon'},\
                'b4057':{'tu':'yjbQR', 'mistake':True, 'reason': 'have yjbQ, first gene in operon'},\
                'b0189':{'tu':'yaeP-rof', 'mistake':False, 'reason': 'have yaeB on the other strand'},\
                'b3865':{'tu':'yihA', 'mistake':False, 'reason': 'have csrC on the other strand'},\
                'b1874':{'tu':'cutC', 'mistake':False, 'reason': 'have cutA on a different operon'},\
                'b3023':{'tu':'ygiV', 'mistake':True, 'reason': 'have ygiW which is first gene in operon'},\
                'b1273':{'tu':'yciN', 'mistake':False, 'reason': 'have yci genes on different operons'},\
                'b1224':{'tu':'narGHJI', 'mistake':True, 'reason': 'have narHJI in the same operon'},\
                'b1143':{'tu':'ymfI', 'mistake':False, 'reason': 'have ymfK nearby but different strand'},\
                'b2290':{'tu':'yfbQ', 'mistake':False, 'reason': 'have yfb genes on different operons'}}

In [87]:

len(unmapped.keys())

Out[87]:

In [50]:

aa = AllTUAnalysis
i = 0
for bnum in s12.index:
    if not ome.query(aa).filter(and_(or_(aa.target1 == 'delta-arcA', aa.target2 == 'delta-arcA'),\
                          or_(aa.target1 == 'wt', aa.target2 == 'wt'), aa.fdr < .05, aa.bnum == bnum,\
                          or_(and_(aa.eacceptor1 == 'anaerobic', aa.eacceptor2 == 'anaerobic'),\
                              and_(aa.eacceptor1 == 'NO3', aa.eacceptor2 == 'NO3'),\
                              and_(aa.eacceptor1 == 'O2', aa.eacceptor2 == 'O2')))).all():
        i+=1
        exp_val = array([x.value for x in ome.query(ExpressionData).filter_by(bnum=bnum).all()]).mean()
        print str(i)+'\t'+bnum+'\t'+str(s12['Operon'].ix[bnum])+'\t'+str(exp_val)

1	b4568	ytjA	nan
2	b4519	icdC	nan
3	b3819	rarD	2.25073529412
4	b2172	yeiQ	2.67014705882
5	b4490	nan	nan
6	b0330	prpR	2.26308823529
7	b1021	pgaABCD	2.69691176471
8	b1534	ydeE	2.47352941176
9	b2152	folE-yeiB	2.25042553191
10	b4512	ybdD	nan
11	b3268	yhdWXYZ	3.29308823529
12	b3324	gspCDEFGHIJKLMO	2.35029411765
13	b1444	ydcW	3.85955882353
14	b4139	aspA	10.0483823529
15	b0527	ybcI	2.25
16	b0319	yahDEFG	2.24088235294
17	b0443	fadM	2.76235294118
18	b0356	frmRAB	9.35617647059
19	b2876	yqeC	2.29205882353
20	b4280	yjhBC	3.69161764706
21	b1223	narK	6.62705882353
22	b2419	yfeKS	2.25340425532
23	b3042	yqiC	11.8351470588
24	b4598	yncL	nan
25	b4057	yjbQR	9.77426470588
26	b0189	yaeP-rof	8.33529411765
27	b3865	yihA	10.1757352941
28	b1874	cutC	4.44808823529
29	b3023	ygiV	6.00823529412
30	b4117	adiA	2.48558823529
31	b4595	yciY	nan
32	b4640	upp-uraA	nan
33	b1273	yciN	5.92852941176
34	b4606	ypfM	nan
35	b1224	narGHJI	9.61558823529
36	b1143	ymfI	7.29411764706
37	b1634	tppB	2.29
38	b4402	yjjY	3.79514705882
39	b1974	yodB	3.06867647059
40	b4641	nan	nan
41	b4589	ylcI	nan
42	b2290	yfbQ	5.15426470588
43	b4115	adiC	2.2685106383

In [56]:

s12

Out[56]:

<class 'pandas.core.frame.DataFrame'>
Index: 229 entries, b0721 to b3491
Data columns (total 6 columns):
Strand         226  non-null values
Operon         227  non-null values
WT             229  non-null values
ΔarcA          229  non-null values
Fold change    229  non-null values
P value        229  non-null values
dtypes: float64(4), object(2)

42/229 not diff expressed in our data 10/43 not measured 20/43 not measurably expressed 13/43 misses 5/13 FP 8 total misses

In [ ]: