First lets take the DEGs from DESeq2 - and transform file to get it read to join with SPIDs
!head /Users/sr320/Dropbox/Steven/eimd/data/deseq2_sig_results.txt
"baseMean" "log2FoldChange" "lfcSE" "stat" "pvalue" "padj" "seastar_clc_contig_10001" 136.27718425946 1.49886855266789 0.550947966456816 2.72052651778936 0.00651780439581695 0.0350101864080016 "seastar_clc_contig_10010" 8.73784349604224 2.43426494953234 0.717338850139719 3.39346593183711 0.000690141423521562 0.00610587057360923 "seastar_clc_contig_10013" 188.603521302622 -1.94923068685006 0.463271107915175 -4.20753777549832 2.58168256856775e-05 0.00041485396609123 "seastar_clc_contig_10045" 50.485024106335 2.87706412205861 0.695003049883772 4.13964244119468 3.47847563039607e-05 0.000526018158180456 "seastar_clc_contig_1005" 3408.98435663456 -1.66691198866687 0.378947946534594 -4.39878881495589 1.08856689786144e-05 0.000199362344222153 "seastar_clc_contig_10050" 276.941589423215 -1.61560402677235 0.323282993601818 -4.9974915437781 5.80808848482353e-07 1.60431884071189e-05 "seastar_clc_contig_1006" 77.8447124150533 -2.01146173192642 0.468218416201358 -4.29599020953798 1.73915258259802e-05 0.000298432523132762 "seastar_clc_contig_10064" 147.578457909919 1.81093710357749 0.683578354090462 2.64920194260252 0.00806821051110654 0.041310905437205 "seastar_clc_contig_10065" 28.5076393455268 2.27188575134493 0.585911374358637 3.87752457243526 0.00010552467251757 0.00131744894528401
!sed 's/"//g' </Users/sr320/Dropbox/Steven/eimd/data/deseq2_sig_results.txt> /Users/sr320/Dropbox/Steven/eimd/data/deseq2_sig_results_a.txt
!head /Users/sr320/Dropbox/Steven/eimd/data/deseq2_sig_results_a.txt
baseMean log2FoldChange lfcSE stat pvalue padj seastar_clc_contig_10001 136.27718425946 1.49886855266789 0.550947966456816 2.72052651778936 0.00651780439581695 0.0350101864080016 seastar_clc_contig_10010 8.73784349604224 2.43426494953234 0.717338850139719 3.39346593183711 0.000690141423521562 0.00610587057360923 seastar_clc_contig_10013 188.603521302622 -1.94923068685006 0.463271107915175 -4.20753777549832 2.58168256856775e-05 0.00041485396609123 seastar_clc_contig_10045 50.485024106335 2.87706412205861 0.695003049883772 4.13964244119468 3.47847563039607e-05 0.000526018158180456 seastar_clc_contig_1005 3408.98435663456 -1.66691198866687 0.378947946534594 -4.39878881495589 1.08856689786144e-05 0.000199362344222153 seastar_clc_contig_10050 276.941589423215 -1.61560402677235 0.323282993601818 -4.9974915437781 5.80808848482353e-07 1.60431884071189e-05 seastar_clc_contig_1006 77.8447124150533 -2.01146173192642 0.468218416201358 -4.29599020953798 1.73915258259802e-05 0.000298432523132762 seastar_clc_contig_10064 147.578457909919 1.81093710357749 0.683578354090462 2.64920194260252 0.00806821051110654 0.041310905437205 seastar_clc_contig_10065 28.5076393455268 2.27188575134493 0.585911374358637 3.87752457243526 0.00010552467251757 0.00131744894528401
#removing header
!tail -n +2 /Users/sr320/Dropbox/Steven/eimd/data/deseq2_sig_results_a.txt > /Users/sr320/Dropbox/Steven/eimd/data/deseq2_sig_results_b.txt
!head /Users/sr320/Dropbox/Steven/eimd/data/deseq2_sig_results_b.txt
seastar_clc_contig_10001 136.27718425946 1.49886855266789 0.550947966456816 2.72052651778936 0.00651780439581695 0.0350101864080016 seastar_clc_contig_10010 8.73784349604224 2.43426494953234 0.717338850139719 3.39346593183711 0.000690141423521562 0.00610587057360923 seastar_clc_contig_10013 188.603521302622 -1.94923068685006 0.463271107915175 -4.20753777549832 2.58168256856775e-05 0.00041485396609123 seastar_clc_contig_10045 50.485024106335 2.87706412205861 0.695003049883772 4.13964244119468 3.47847563039607e-05 0.000526018158180456 seastar_clc_contig_1005 3408.98435663456 -1.66691198866687 0.378947946534594 -4.39878881495589 1.08856689786144e-05 0.000199362344222153 seastar_clc_contig_10050 276.941589423215 -1.61560402677235 0.323282993601818 -4.9974915437781 5.80808848482353e-07 1.60431884071189e-05 seastar_clc_contig_1006 77.8447124150533 -2.01146173192642 0.468218416201358 -4.29599020953798 1.73915258259802e-05 0.000298432523132762 seastar_clc_contig_10064 147.578457909919 1.81093710357749 0.683578354090462 2.64920194260252 0.00806821051110654 0.041310905437205 seastar_clc_contig_10065 28.5076393455268 2.27188575134493 0.585911374358637 3.87752457243526 0.00010552467251757 0.00131744894528401 seastar_clc_contig_10074 13.7264378211451 1.57931966078503 0.609122521040588 2.59277831016167 0.0095204116954605 0.0468152722934354
!sed 's/seastar/Phel/g' </Users/sr320/Dropbox/Steven/eimd/data/deseq2_sig_results_b.txt> /Users/sr320/Dropbox/Steven/eimd/data/deseq2_sig_results_c.txt
!head /Users/sr320/Dropbox/Steven/eimd/data/deseq2_sig_results_c.txt
Phel_clc_contig_10001 136.27718425946 1.49886855266789 0.550947966456816 2.72052651778936 0.00651780439581695 0.0350101864080016 Phel_clc_contig_10010 8.73784349604224 2.43426494953234 0.717338850139719 3.39346593183711 0.000690141423521562 0.00610587057360923 Phel_clc_contig_10013 188.603521302622 -1.94923068685006 0.463271107915175 -4.20753777549832 2.58168256856775e-05 0.00041485396609123 Phel_clc_contig_10045 50.485024106335 2.87706412205861 0.695003049883772 4.13964244119468 3.47847563039607e-05 0.000526018158180456 Phel_clc_contig_1005 3408.98435663456 -1.66691198866687 0.378947946534594 -4.39878881495589 1.08856689786144e-05 0.000199362344222153 Phel_clc_contig_10050 276.941589423215 -1.61560402677235 0.323282993601818 -4.9974915437781 5.80808848482353e-07 1.60431884071189e-05 Phel_clc_contig_1006 77.8447124150533 -2.01146173192642 0.468218416201358 -4.29599020953798 1.73915258259802e-05 0.000298432523132762 Phel_clc_contig_10064 147.578457909919 1.81093710357749 0.683578354090462 2.64920194260252 0.00806821051110654 0.041310905437205 Phel_clc_contig_10065 28.5076393455268 2.27188575134493 0.585911374358637 3.87752457243526 0.00010552467251757 0.00131744894528401 Phel_clc_contig_10074 13.7264378211451 1.57931966078503 0.609122521040588 2.59277831016167 0.0095204116954605 0.0468152722934354
#file downloaded from SQLshare join
!head /Users/sr320/Dropbox/Steven/eimd/data/Phel_Deseq_SP.csv
!tr ',' "\t" </Users/sr320/Dropbox/Steven/eimd/data/Phel_Deseq_SP.csv> /Users/sr320/Dropbox/Steven/eimd/data/Phel_Deseq_SP.txt
!head /Users/sr320/Dropbox/Steven/eimd/data/Phel_Deseq_SP.txt
!awk '{print $10}' /Users/sr320/Dropbox/Steven/eimd/data/Phel_Deseq_SP.txt
Column3 Q5R7A2 P22232 Q5RC04 P97433 O81884 Q6GNG8 Q8BZQ7 P04176 Q7T010 Q9Y566 Q13454 Q8R151 P17560 Q96QF0 P23787 Q92EK7 P14316 P00125 Q8C172 P23824 O15091 A0JP86 P34147 Q91V92 Q4G0U5 Q9W2N0 Q5QJE6 Q5RFI8 Q9H3F6 Q9WU22 Q15485 Q9QX47 Q96PB1 Q6NZJ6 Q9CZP0 Q689D1 A2AVA0 Q9NYB5 Q95R48 P20690 Q9DFZ4 P48601 Q32KI9 Q9P0J7 Q68CZ1 O60285 Q96LD8 P10809 Q3UDK1 P61082 Q61824 O14807 P30937 Q9V3D2 Q7L622 Q7Z2H8 O15072 Q4KMD3 Q7ZUX3 O15027 Q8BZM1 Q5R5C9 Q49B93 Q99536 O57478 Q9UGM3 Q9Y4P3 Q96P48 Q8BG30 Q8P3H1 Q29RI0 A5GFY8 Q9JJ46 P21328 P09960 P13280 Q866N2 Q6DDK2 Q9NJ15 Q54HH2 C3XVT5 Q0D4Z6 Q9BX84 F7J220 Q6EE31 Q5EB73 Q8BZ20 Q6B4U9 P10768 Q6PC64 Q28EX9 Q6NWH0 E1C231 Q2KJC9 Q95NR9 P20070 Q9U5L1 P29074 Q9UGM6 O15335 P54802 Q8BGV4 P22682 Q8VE22 Q9C0D6 P79761 Q8IWY4 O75936 O35717 Q3TYE7 Q5BL72 P58682 P0CC00 Q8BYK4 P84104 Q29503 Q5E985 Q7LL04 Q924W7 Q9H2U1 Q9JIX8 Q9Z108 Q9JME2 P15170 Q99LB0 O95478 Q8IZJ3 Q2TBI2 Q9DCN1 Q9BY84 Q3UKU1 Q9NYB5 Q13217 Q9GZU5 Q9W735 Q9D8N3 Q9Y5Q9 P43141 Q63369 O84402 Q8BMN4 Q62867 Q9Y223 Q8N0X4 Q62448 Q86TV6 Q9H477 Q9GR88 Q99K85 P23978 P33945 P14133 Q9HCB6 Q8VCN5 Q58EM4 O05218 P09848 Q96AB6 Q6P4R8 Q80U30 Q8N954 Q0P4S0 Q5NVI9 P49088 Q00945 Q7ZUK7 Q01664 Q9BYK8 Q8BJ03 Q9H981 Q3SY69 Q13045 P70541 Q4PLW0 P08635 Q6A009 Q0V9E9 Q8IVF7 Q8K1T0 Q28FF3 P40937 O60879 Q96PS8 Q566I3 Q9DBN5 O43426 Q8TAQ5 Q2LAM0 Q923E4 P25325 P80147 A5D6U8 Q06806 Q6IP59 P28622 Q5RAH7 P21333 Q9TU03 Q9V3H2 Q9H0H3 Q08E66 Q62448 Q5PRC1 Q7TMS5 Q1LZI2 O60315 Q8WVM7 Q96BD6 P06027 Q8I7P9 Q02372 Q8AVG9 P70549 P11029 Q5RD64 P09215 Q9ULZ9 Q561R7 Q2KIA4 P09324 Q9NZJ4 Q5R4J5 Q9JM76 P11584 Q5U508 Q9EQJ0 Q8BX05 Q94738 Q4KMI4 Q3SYW2 Q96MC6 Q95XZ6 Q6IN84 Q0D4Z6 Q90593 Q04861 P46023 Q5ZKR7 Q5NVI9 O00482 Q9Y620 P55115 Q5I0J5 Q99676 D0Z9R0 Q80XC3 Q92562 O76082 P53445 D4A1J4 Q6GNQ1 Q5R8Z8 A7MB54 P23471 Q54KA7 O13016 O94985 Q9Y223 P51644 P29054 Q9JI19 P81601 Q9D994 Q60803 O75351 P21836 Q3ZBG9 Q6P5E4 O61367 Q3SYS9 Q1JP75 Q80W93 Q9TR36 Q9H3S4 Q5R511 Q9UKG1 P97379 Q96EV8 Q9NR30 Q5SRX1 Q8WXX0 Q5R6X7 A2APV2 P49109 Q7ZYC4 Q29499 Q05423 Q5RGJ5 Q9VTK2 Q9GZT4 Q8BYK4 Q4R5V2 Q9DAK2 Q7TQI7 Q90ZC7 Q8WX92 Q0ZDF7 Q9ES00 Q5ZJR8 Q9GKX2 O75343 Q6DJI9 Q9UGM3 P49013 Q5ZL67 Q28727 Q5R9A7 A2VDS1 Q9Y2Q0 Q1RMR4 P07872 O60879 Q3ZBR5 Q28BM0 Q6DJ06 Q8JFP1 A5HNF6 Q9D0K0 Q9W539 P70473 P96202 Q9BXW4 Q5U5V2 Q7TNG8 O70497 O14874 Q29261 O14512 B6P4U0 Q6DCX5 Q5XIR6 C3YWU0 Q6DEL2 B5DEQ3 O02833 P26884 Q4QQW3 Q8JIY1 Q5ZIV1 P30838 Q8K4L3 P91620 Q61187 O77245 P13216 Q9UH65 Q9V3G7 Q6UWV6 Q5BLE8 D3ZPX4 Q5RED8 P91119 P51617 Q04832 Q13951 Q90889 A2RSQ0 Q6P8M1 Q8TCT9 Q6Y1H2 Q15032 Q8TDX6 P00919 Q90744 Q99943 P46058 F6P3G4 Q9BG94 P80404 Q7T2A5 Q9WTR0 Q9WU78 Q9BVH7 Q28DL4 Q9BXM7 Q7LHG5 Q8K370 Q5F371 Q5T160 P21328 P97717 Q7ZWZ5 P21129 Q2NL31 Q2HJI3 Q94738 Q2IBC0 Q4R5G7 Q3ZBD2 Q4KLA0 P11475 P61460 Q6UX65 Q00651 Q6PFR5 P14380 E1C7T6 Q71U34 Q6PB06 P28072 Q28D84 Q8N5H7 P54319 A3KGZ2 P47736 P41932 Q86XE3 Q9NQZ8 A2BGL3 Q8TC12 Q9VCA2 Q5F3Z9 P34885 Q6PFQ2 P48818 Q60HF3 Q9DCT5 Q4JIM4 Q8C0I1 O88281 Q9TUG2 Q6KCD5 Q6ZUX7 Q7Z7L9 C3YFB4 Q5RD64 Q5ZL42 P61799 P50169 Q5U4S8 Q9GZR5 Q8R0A7 Q6DD06 O59028 Q8HYJ4 P55036 P49615 O75486 P41386 Q61321 P97524 Q2HJ57 Q5M8V8 Q6KAR6 P28175 Q00612 A9MH27 Q86GC8 Q9DBB9 Q09575 A0JM12 Q17QJ5 Q9Z2K9 Q9HAC7 Q0VA61 P04323 Q8K4T5 P30042 Q5ZIJ9 Q4V8S3 P08594 Q29RH4 Q0D2E8 Q9BWU0 Q8BGC3 O95238 Q8F7W8 Q5ZL23 Q8WU17 P28480 O68965 Q9UGM3 Q6PCS4 P0CG13 P13073 Q32LN0 Q8VEM8 Q6P268 Q9VZS3 P35978 Q91VS7 Q3UMR5 Q3V1H3 Q6NRW5 Q5ZLY5 Q96P53 Q54BU4 Q6DNG6 Q6ZT12 Q9XY07 P82251 Q9NTM9 Q9BUD6 Q9W4P5 B0BN95 Q21974 Q96BT7 Q07352 O54715 Q90YK5 P05708 Q5RDQ8 Q8K4S1 P00389 Q0VA16 P24899 Q8K4C0 P11029 Q6PHY8 Q9Y5Y0 Q9H0E2 Q16644 Q38SD2 Q03347 Q7ZUP1 Q9U539 P98156 O95260 O77656 Q80VW7 P31403 P91660 P15505 P41148 Q5RCC9 Q1LZB6 Q99N02 Q8BHT7 Q921M3 Q90368 P14733 Q7ZVN7 Q00685 Q86Y82 Q9QYJ0 Q28HN4 Q91754 Q64319 Q8IUX8 B7ZCC9 Q6NS52 Q98TX3 Q5R5V4 Q55E72 P42768 Q3ZCH0 Q90XD2 P05689 A2VDP6 Q8MPM1 P26932 Q9PWA0 P60901 P53395 O35344 Q5EAJ7 P48809 P52209 Q90Z16 Q6N021 Q503Y7 Q06496 Q9QYM0 Q9NX74 B1H116 Q8BHR2 Q8BKC5 P21522 P62335 Q8MJU9 P15104 P28863 Q9DDT2 O55057 P41234 Q6RUV5 Q641Z2 Q969X5 Q6NZW8 Q5F495 Q5UQP2 Q9BYK8 Q99LE6 P48437 B5DE73 P49585 Q8VEL2 P59723 Q96RW7 Q9BQA9 Q5GLH2 A0PYP3 P41233 Q9ESG5 Q8BGZ4 Q8HYL8 Q9DC23 Q29041 Q5HYK7 Q75J93 O43679 P15170 Q17QH8 Q6UWM7 Q8R0S2 P94681 P62321 Q8TEY5 Q08209 Q63505 Q4KM79 A4VPC3 P18395 P40792 Q3ZBH0 Q55E72 P35822 Q9Z2F6 Q6GM82 Q86XA9 Q99L45 Q26534 Q29611 P62262 Q9UGJ0 Q91WM2 Q8QFP8 P11029 Q90673 Q5DC69 P11029 O75832 Q9WV52 Q9N0P9 Q5MB13 P53804 P59325 Q6AZN6 Q0V9N0 Q9VGY6 A4IIW7 Q8BYI9 Q6PBA2 B2GUZ1 Q8BGT0 P82343 P21912 Q9SEV0 Q8IUR6 Q13905 Q7YS91 Q69BJ8 O35920 Q8TDQ7 Q91VN6 Q3T0K2 Q5RFR0 P31319 Q6NU98 Q9XY07 Q08BU1 P16393 Q0V8H6 Q5ND34 Q01063 Q99615 Q5ZJU3 O54988 Q561L1 Q16822 Q6DGF4 O35464 Q32NH8 O60271 Q5RCS0 P42357 Q40784 P14198 Q6P8E9 Q9JI08 P0C6B8 O00303 Q0P563 P41743 Q96RW7 Q29504 Q8NBN7 Q71U34 Q6PAX7 Q5U2S1 Q5U3Y5 Q9D8N6 Q8N695 P54612 P55345 Q91Z92 Q4KLG9 Q503L9 A9UMS3 Q13371 Q91V16 Q91YE3 Q9YHT4 A8E7G4 Q9VZI3 Q9IB84 Q2KI54 Q92544 Q5I085 Q9GL24 Q7LL04 Q7SXS8 Q8AWF2 P42125 P54725 P30622 O95155 Q4R4Q6 Q9UM22 P21580 A4IF63 Q91YR1 P23004 Q91175 Q99M80 P42577 Q9BT23 Q5R481 P41971 Q8SQC1 O55029 Q58A42 Q80W94 O73817 A7Y2W8 E1BPN0 Q5MJS3 Q9VZ23 Q5R5U1 Q6NY73 Q9JMD3 Q1KKZ1 Q64I00 Q9U943 Q5ZLX2 Q9WVA3 P54613 A2AVA0 P10079 Q498L0 Q9HB07 Q9D2Y4 Q4R562 Q32KH5 P13716 Q8BV79 Q7ZVZ7 Q9R144 Q6UB99 Q9Y2F5 O54981 P00367 Q1LUT1 Q9DBG7 O95628 Q9R0S2 O08700 Q5RB40 O14522 Q4AEH5 Q9HBY0 Q9Z2U1 Q6PC91 Q3TZM9 Q8BW10 P54814 Q5RBP9 Q5VVW2 Q7SIB2 Q5F418 Q5F418 P49138 P01024 Q96RW7 P27169 P26638 Q29384 Q5JR59 Q66HR2 Q99M80 Q8IY22 Q9BYK8 Q8JG30 P46952 Q9WUN2 Q1HG43 P53992 Q9UQ35 Q9NVP1 Q9UKP5 P05183 Q63159 O43242 Q9PTW9 P97280 Q8N5U6 E1BK52 Q869V1 O54750 O54694 Q9UDY8 Q91Z46 P78382 O00232 P63155 Q6PCJ9 Q5R4F4 Q12719 P23975 Q24322 Q501L1 P28271 P46471 P09917 Q5ZKM1 Q66HA4 Q9VBW3 P02740 Q62829 Q3SZX8 Q923V4 Q8VDM4 Q3T102 Q3ZBD0 Q9XT26 Q5F3L9 Q5RE48 P53671 P35223 Q28F07 P27463 O43196 Q14344 Q2LAP6 Q09575 Q8JHE9 Q7Z449 P51821 Q8BIE6 Q5RFU0 Q24322 Q9U943 P08761 P31404 Q9Z2J0 Q6ZMW2 P04642 Q80V70 Q9ESE1 Q29RV1 Q3MHL7 O88377 P18652 Q9QZU7 Q90687 P00687 Q5I0R4 Q6P823 Q5XHI2 Q6GL11 P52435 B3STU3 Q9CA28 P08582 Q09225 Q29RM1 P19182 Q99L28 Q61469 O08992 Q94738 Q9HAB8 Q12888 Q32NT4 O35488 Q6DRC4 O95164 Q9TZM3 Q6DK91 Q5E9H5 Q15485 Q9U8W7 Q9UBI9 Q99MN1 O54748 A4II46 O35887 Q9WTR6 Q28199 P54714 P56489 Q5E9S4 P33947 Q15599 Q32KH9 P56520 O75594 Q22165 Q4R6V2 Q0GGW5 P11611 Q08E38 A8WGF7 Q6ZV73 Q9HAR2 Q66T02 P26262 Q6TUG0 Q54TR1 O95786 Q9C0A0 P25867 Q5QQ56 Q6NVU2 Q5M7F8 Q60722 Q5HZQ9 A7RM20 P00029 P13010 Q9BZE4 Q5R7J6 Q8CD54 Q60803 P11501 O00567 Q6PEC4 Q13702 Q3ZMH1 P27117 Q0VD26 Q6AYQ8 Q6PJ21 P70388 O88831 P33497 Q2T9X2 P54632 Q94887 D3ZVP7 Q60855 Q6DHL4 Q14155 P28648 Q75JF3 P53619 Q21828 Q6PEH8 Q5ZL55 Q9Y2D8 P05689 Q5ZJZ5 Q9CPX9 Q99958 Q8R367 P41383 Q9CX98 O46373 Q5EB77 Q9DB05 P08775 Q0MVN8 P54611 Q9H3S7 Q9NZR2 Q6VAB6 Q66JF3 Q62760 Q06805 Q6GQ29 Q761V0 A4IGP0 A2AAY5 P25788 B0FYY4 Q5ZJK8 Q0VFD8 Q8N264 Q29RN6 Q9UHD2 P21328 Q5RAV6 P19440 Q8WWW0 Q8BX70 Q6RUV5 O05408 P16444 Q8TE73 Q9MYM7 Q8K268 Q6FHJ7 Q5I0I9 Q68F72 Q9H0W9 Q9BYN7 Q7Z449 P35604 Q54F25 P08953 Q6NYE2 Q5RB37 Q9UNN5 Q5PQS6 Q8N960 Q86VP3 Q60636 Q9QUR6 Q91090 Q9UPR0 P81134 Q9N2I9 Q2I6J1 O15118 Q14588 P10160 A5D8M6 Q8BGC9
!awk '{print $10}' /Users/sr320/Dropbox/Steven/eimd/data/Phel_Deseq_SP.txt | uniq
Column3 Q5R7A2 P22232 Q5RC04 P97433 O81884 Q6GNG8 Q8BZQ7 P04176 Q7T010 Q9Y566 Q13454 Q8R151 P17560 Q96QF0 P23787 Q92EK7 P14316 P00125 Q8C172 P23824 O15091 A0JP86 P34147 Q91V92 Q4G0U5 Q9W2N0 Q5QJE6 Q5RFI8 Q9H3F6 Q9WU22 Q15485 Q9QX47 Q96PB1 Q6NZJ6 Q9CZP0 Q689D1 A2AVA0 Q9NYB5 Q95R48 P20690 Q9DFZ4 P48601 Q32KI9 Q9P0J7 Q68CZ1 O60285 Q96LD8 P10809 Q3UDK1 P61082 Q61824 O14807 P30937 Q9V3D2 Q7L622 Q7Z2H8 O15072 Q4KMD3 Q7ZUX3 O15027 Q8BZM1 Q5R5C9 Q49B93 Q99536 O57478 Q9UGM3 Q9Y4P3 Q96P48 Q8BG30 Q8P3H1 Q29RI0 A5GFY8 Q9JJ46 P21328 P09960 P13280 Q866N2 Q6DDK2 Q9NJ15 Q54HH2 C3XVT5 Q0D4Z6 Q9BX84 F7J220 Q6EE31 Q5EB73 Q8BZ20 Q6B4U9 P10768 Q6PC64 Q28EX9 Q6NWH0 E1C231 Q2KJC9 Q95NR9 P20070 Q9U5L1 P29074 Q9UGM6 O15335 P54802 Q8BGV4 P22682 Q8VE22 Q9C0D6 P79761 Q8IWY4 O75936 O35717 Q3TYE7 Q5BL72 P58682 P0CC00 Q8BYK4 P84104 Q29503 Q5E985 Q7LL04 Q924W7 Q9H2U1 Q9JIX8 Q9Z108 Q9JME2 P15170 Q99LB0 O95478 Q8IZJ3 Q2TBI2 Q9DCN1 Q9BY84 Q3UKU1 Q9NYB5 Q13217 Q9GZU5 Q9W735 Q9D8N3 Q9Y5Q9 P43141 Q63369 O84402 Q8BMN4 Q62867 Q9Y223 Q8N0X4 Q62448 Q86TV6 Q9H477 Q9GR88 Q99K85 P23978 P33945 P14133 Q9HCB6 Q8VCN5 Q58EM4 O05218 P09848 Q96AB6 Q6P4R8 Q80U30 Q8N954 Q0P4S0 Q5NVI9 P49088 Q00945 Q7ZUK7 Q01664 Q9BYK8 Q8BJ03 Q9H981 Q3SY69 Q13045 P70541 Q4PLW0 P08635 Q6A009 Q0V9E9 Q8IVF7 Q8K1T0 Q28FF3 P40937 O60879 Q96PS8 Q566I3 Q9DBN5 O43426 Q8TAQ5 Q2LAM0 Q923E4 P25325 P80147 A5D6U8 Q06806 Q6IP59 P28622 Q5RAH7 P21333 Q9TU03 Q9V3H2 Q9H0H3 Q08E66 Q62448 Q5PRC1 Q7TMS5 Q1LZI2 O60315 Q8WVM7 Q96BD6 P06027 Q8I7P9 Q02372 Q8AVG9 P70549 P11029 Q5RD64 P09215 Q9ULZ9 Q561R7 Q2KIA4 P09324 Q9NZJ4 Q5R4J5 Q9JM76 P11584 Q5U508 Q9EQJ0 Q8BX05 Q94738 Q4KMI4 Q3SYW2 Q96MC6 Q95XZ6 Q6IN84 Q0D4Z6 Q90593 Q04861 P46023 Q5ZKR7 Q5NVI9 O00482 Q9Y620 P55115 Q5I0J5 Q99676 D0Z9R0 Q80XC3 Q92562 O76082 P53445 D4A1J4 Q6GNQ1 Q5R8Z8 A7MB54 P23471 Q54KA7 O13016 O94985 Q9Y223 P51644 P29054 Q9JI19 P81601 Q9D994 Q60803 O75351 P21836 Q3ZBG9 Q6P5E4 O61367 Q3SYS9 Q1JP75 Q80W93 Q9TR36 Q9H3S4 Q5R511 Q9UKG1 P97379 Q96EV8 Q9NR30 Q5SRX1 Q8WXX0 Q5R6X7 A2APV2 P49109 Q7ZYC4 Q29499 Q05423 Q5RGJ5 Q9VTK2 Q9GZT4 Q8BYK4 Q4R5V2 Q9DAK2 Q7TQI7 Q90ZC7 Q8WX92 Q0ZDF7 Q9ES00 Q5ZJR8 Q9GKX2 O75343 Q6DJI9 Q9UGM3 P49013 Q5ZL67 Q28727 Q5R9A7 A2VDS1 Q9Y2Q0 Q1RMR4 P07872 O60879 Q3ZBR5 Q28BM0 Q6DJ06 Q8JFP1 A5HNF6 Q9D0K0 Q9W539 P70473 P96202 Q9BXW4 Q5U5V2 Q7TNG8 O70497 O14874 Q29261 O14512 B6P4U0 Q6DCX5 Q5XIR6 C3YWU0 Q6DEL2 B5DEQ3 O02833 P26884 Q4QQW3 Q8JIY1 Q5ZIV1 P30838 Q8K4L3 P91620 Q61187 O77245 P13216 Q9UH65 Q9V3G7 Q6UWV6 Q5BLE8 D3ZPX4 Q5RED8 P91119 P51617 Q04832 Q13951 Q90889 A2RSQ0 Q6P8M1 Q8TCT9 Q6Y1H2 Q15032 Q8TDX6 P00919 Q90744 Q99943 P46058 F6P3G4 Q9BG94 P80404 Q7T2A5 Q9WTR0 Q9WU78 Q9BVH7 Q28DL4 Q9BXM7 Q7LHG5 Q8K370 Q5F371 Q5T160 P21328 P97717 Q7ZWZ5 P21129 Q2NL31 Q2HJI3 Q94738 Q2IBC0 Q4R5G7 Q3ZBD2 Q4KLA0 P11475 P61460 Q6UX65 Q00651 Q6PFR5 P14380 E1C7T6 Q71U34 Q6PB06 P28072 Q28D84 Q8N5H7 P54319 A3KGZ2 P47736 P41932 Q86XE3 Q9NQZ8 A2BGL3 Q8TC12 Q9VCA2 Q5F3Z9 P34885 Q6PFQ2 P48818 Q60HF3 Q9DCT5 Q4JIM4 Q8C0I1 O88281 Q9TUG2 Q6KCD5 Q6ZUX7 Q7Z7L9 C3YFB4 Q5RD64 Q5ZL42 P61799 P50169 Q5U4S8 Q9GZR5 Q8R0A7 Q6DD06 O59028 Q8HYJ4 P55036 P49615 O75486 P41386 Q61321 P97524 Q2HJ57 Q5M8V8 Q6KAR6 P28175 Q00612 A9MH27 Q86GC8 Q9DBB9 Q09575 A0JM12 Q17QJ5 Q9Z2K9 Q9HAC7 Q0VA61 P04323 Q8K4T5 P30042 Q5ZIJ9 Q4V8S3 P08594 Q29RH4 Q0D2E8 Q9BWU0 Q8BGC3 O95238 Q8F7W8 Q5ZL23 Q8WU17 P28480 O68965 Q9UGM3 Q6PCS4 P0CG13 P13073 Q32LN0 Q8VEM8 Q6P268 Q9VZS3 P35978 Q91VS7 Q3UMR5 Q3V1H3 Q6NRW5 Q5ZLY5 Q96P53 Q54BU4 Q6DNG6 Q6ZT12 Q9XY07 P82251 Q9NTM9 Q9BUD6 Q9W4P5 B0BN95 Q21974 Q96BT7 Q07352 O54715 Q90YK5 P05708 Q5RDQ8 Q8K4S1 P00389 Q0VA16 P24899 Q8K4C0 P11029 Q6PHY8 Q9Y5Y0 Q9H0E2 Q16644 Q38SD2 Q03347 Q7ZUP1 Q9U539 P98156 O95260 O77656 Q80VW7 P31403 P91660 P15505 P41148 Q5RCC9 Q1LZB6 Q99N02 Q8BHT7 Q921M3 Q90368 P14733 Q7ZVN7 Q00685 Q86Y82 Q9QYJ0 Q28HN4 Q91754 Q64319 Q8IUX8 B7ZCC9 Q6NS52 Q98TX3 Q5R5V4 Q55E72 P42768 Q3ZCH0 Q90XD2 P05689 A2VDP6 Q8MPM1 P26932 Q9PWA0 P60901 P53395 O35344 Q5EAJ7 P48809 P52209 Q90Z16 Q6N021 Q503Y7 Q06496 Q9QYM0 Q9NX74 B1H116 Q8BHR2 Q8BKC5 P21522 P62335 Q8MJU9 P15104 P28863 Q9DDT2 O55057 P41234 Q6RUV5 Q641Z2 Q969X5 Q6NZW8 Q5F495 Q5UQP2 Q9BYK8 Q99LE6 P48437 B5DE73 P49585 Q8VEL2 P59723 Q96RW7 Q9BQA9 Q5GLH2 A0PYP3 P41233 Q9ESG5 Q8BGZ4 Q8HYL8 Q9DC23 Q29041 Q5HYK7 Q75J93 O43679 P15170 Q17QH8 Q6UWM7 Q8R0S2 P94681 P62321 Q8TEY5 Q08209 Q63505 Q4KM79 A4VPC3 P18395 P40792 Q3ZBH0 Q55E72 P35822 Q9Z2F6 Q6GM82 Q86XA9 Q99L45 Q26534 Q29611 P62262 Q9UGJ0 Q91WM2 Q8QFP8 P11029 Q90673 Q5DC69 P11029 O75832 Q9WV52 Q9N0P9 Q5MB13 P53804 P59325 Q6AZN6 Q0V9N0 Q9VGY6 A4IIW7 Q8BYI9 Q6PBA2 B2GUZ1 Q8BGT0 P82343 P21912 Q9SEV0 Q8IUR6 Q13905 Q7YS91 Q69BJ8 O35920 Q8TDQ7 Q91VN6 Q3T0K2 Q5RFR0 P31319 Q6NU98 Q9XY07 Q08BU1 P16393 Q0V8H6 Q5ND34 Q01063 Q99615 Q5ZJU3 O54988 Q561L1 Q16822 Q6DGF4 O35464 Q32NH8 O60271 Q5RCS0 P42357 Q40784 P14198 Q6P8E9 Q9JI08 P0C6B8 O00303 Q0P563 P41743 Q96RW7 Q29504 Q8NBN7 Q71U34 Q6PAX7 Q5U2S1 Q5U3Y5 Q9D8N6 Q8N695 P54612 P55345 Q91Z92 Q4KLG9 Q503L9 A9UMS3 Q13371 Q91V16 Q91YE3 Q9YHT4 A8E7G4 Q9VZI3 Q9IB84 Q2KI54 Q92544 Q5I085 Q9GL24 Q7LL04 Q7SXS8 Q8AWF2 P42125 P54725 P30622 O95155 Q4R4Q6 Q9UM22 P21580 A4IF63 Q91YR1 P23004 Q91175 Q99M80 P42577 Q9BT23 Q5R481 P41971 Q8SQC1 O55029 Q58A42 Q80W94 O73817 A7Y2W8 E1BPN0 Q5MJS3 Q9VZ23 Q5R5U1 Q6NY73 Q9JMD3 Q1KKZ1 Q64I00 Q9U943 Q5ZLX2 Q9WVA3 P54613 A2AVA0 P10079 Q498L0 Q9HB07 Q9D2Y4 Q4R562 Q32KH5 P13716 Q8BV79 Q7ZVZ7 Q9R144 Q6UB99 Q9Y2F5 O54981 P00367 Q1LUT1 Q9DBG7 O95628 Q9R0S2 O08700 Q5RB40 O14522 Q4AEH5 Q9HBY0 Q9Z2U1 Q6PC91 Q3TZM9 Q8BW10 P54814 Q5RBP9 Q5VVW2 Q7SIB2 Q5F418 P49138 P01024 Q96RW7 P27169 P26638 Q29384 Q5JR59 Q66HR2 Q99M80 Q8IY22 Q9BYK8 Q8JG30 P46952 Q9WUN2 Q1HG43 P53992 Q9UQ35 Q9NVP1 Q9UKP5 P05183 Q63159 O43242 Q9PTW9 P97280 Q8N5U6 E1BK52 Q869V1 O54750 O54694 Q9UDY8 Q91Z46 P78382 O00232 P63155 Q6PCJ9 Q5R4F4 Q12719 P23975 Q24322 Q501L1 P28271 P46471 P09917 Q5ZKM1 Q66HA4 Q9VBW3 P02740 Q62829 Q3SZX8 Q923V4 Q8VDM4 Q3T102 Q3ZBD0 Q9XT26 Q5F3L9 Q5RE48 P53671 P35223 Q28F07 P27463 O43196 Q14344 Q2LAP6 Q09575 Q8JHE9 Q7Z449 P51821 Q8BIE6 Q5RFU0 Q24322 Q9U943 P08761 P31404 Q9Z2J0 Q6ZMW2 P04642 Q80V70 Q9ESE1 Q29RV1 Q3MHL7 O88377 P18652 Q9QZU7 Q90687 P00687 Q5I0R4 Q6P823 Q5XHI2 Q6GL11 P52435 B3STU3 Q9CA28 P08582 Q09225 Q29RM1 P19182 Q99L28 Q61469 O08992 Q94738 Q9HAB8 Q12888 Q32NT4 O35488 Q6DRC4 O95164 Q9TZM3 Q6DK91 Q5E9H5 Q15485 Q9U8W7 Q9UBI9 Q99MN1 O54748 A4II46 O35887 Q9WTR6 Q28199 P54714 P56489 Q5E9S4 P33947 Q15599 Q32KH9 P56520 O75594 Q22165 Q4R6V2 Q0GGW5 P11611 Q08E38 A8WGF7 Q6ZV73 Q9HAR2 Q66T02 P26262 Q6TUG0 Q54TR1 O95786 Q9C0A0 P25867 Q5QQ56 Q6NVU2 Q5M7F8 Q60722 Q5HZQ9 A7RM20 P00029 P13010 Q9BZE4 Q5R7J6 Q8CD54 Q60803 P11501 O00567 Q6PEC4 Q13702 Q3ZMH1 P27117 Q0VD26 Q6AYQ8 Q6PJ21 P70388 O88831 P33497 Q2T9X2 P54632 Q94887 D3ZVP7 Q60855 Q6DHL4 Q14155 P28648 Q75JF3 P53619 Q21828 Q6PEH8 Q5ZL55 Q9Y2D8 P05689 Q5ZJZ5 Q9CPX9 Q99958 Q8R367 P41383 Q9CX98 O46373 Q5EB77 Q9DB05 P08775 Q0MVN8 P54611 Q9H3S7 Q9NZR2 Q6VAB6 Q66JF3 Q62760 Q06805 Q6GQ29 Q761V0 A4IGP0 A2AAY5 P25788 B0FYY4 Q5ZJK8 Q0VFD8 Q8N264 Q29RN6 Q9UHD2 P21328 Q5RAV6 P19440 Q8WWW0 Q8BX70 Q6RUV5 O05408 P16444 Q8TE73 Q9MYM7 Q8K268 Q6FHJ7 Q5I0I9 Q68F72 Q9H0W9 Q9BYN7 Q7Z449 P35604 Q54F25 P08953 Q6NYE2 Q5RB37 Q9UNN5 Q5PQS6 Q8N960 Q86VP3 Q60636 Q9QUR6 Q91090 Q9UPR0 P81134 Q9N2I9 Q2I6J1 O15118 Q14588 P10160 A5D8M6 Q8BGC9
!wc -l /Users/sr320/Dropbox/Steven/eimd/data/Phel_Deseq_SP.txt
3915 /Users/sr320/Dropbox/Steven/eimd/data/Phel_Deseq_SP.txt
!head /Users/sr320/Dropbox/Steven/eimd/data/Phel_clc_blastx_uniprot_sprot_sqlready.tab
Phel_clc_contig_4 sp P25001 COX1_PISOC 88.39 517 48 1 7061 5547 1 517 0.0 749 Phel_clc_contig_7 sp Q33818 CYB_ASTPE 79.94 329 66 0 993 7 51 379 9e-168 479 Phel_clc_contig_8 sp P68037 UB2L3_MOUSE 76.97 152 35 0 4862 4407 1 152 7e-62 214 Phel_clc_contig_9 sp Q0MVN8 QOR_PIG 45.61 239 129 1 796 80 90 327 5e-63 210 Phel_clc_contig_17 sp Q6DGL8 RT15_DANRE 35.00 180 107 3 1177 638 61 230 5e-22 99.8 Phel_clc_contig_18 sp P96202 PPSC_MYCTU 30.81 714 438 15 5407 3386 1414 2111 6e-76 286 Phel_clc_contig_20 sp P46058 EDSP_CYNPY 31.03 348 218 8 1731 703 4 334 5e-38 148 Phel_clc_contig_22 sp Q96LI5 CNO6L_HUMAN 60.78 357 128 5 1887 832 186 535 2e-149 450 Phel_clc_contig_24 sp P63245 GBLP_RAT 80.77 312 60 0 1032 97 1 312 0.0 540 Phel_clc_contig_25 sp Q9QYP1 LRP4_RAT 32.74 623 393 7 1816 5 393 1008 1e-99 339
!awk '{print $3}' /Users/sr320/Dropbox/Steven/eimd/data/blast_output/Phel_clc_blastx_uniprot_sprot_sqlready.tab | pbcopy
Add gene list and background to DAVID
pwd
u'/Users/sr320/Dropbox/Steven/eimd/ipynbs'
cd ..
/Users/sr320/Dropbox/Steven/eimd
cd data
/Users/sr320/Dropbox/Steven/eimd/data
!curl -O http://david.abcc.ncifcrf.gov/data/download/chart_EA61531C2B4A1407365629460.txt
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 75765 100 75765 0 0 119k 0 --:--:-- --:--:-- --:--:-- 137k
!head chart_EA61531C2B4A1407365629460.txt
Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR GOTERM_BP_FAT GO:0002253~activation of immune response 12 1.3157894736842104 2.217491937683056E-7 Q3SYW2, Q9WUN2, P10809, P51617, Q15485, Q00685, O70497, Q689D1, Q29041, P01024, Q9UDY8, Q4JIM4 700 16 5680 6.085714285714285 5.83473655758171E-4 5.83473655758171E-4 3.9347673449485754E-4 GOTERM_BP_FAT GO:0045087~innate immune response 15 1.644736842105263 8.977598174254794E-6 Q9UGM3, Q9UHD2, Q15485, Q00685, O70497, Q29041, Q689D1, Q9UDY8, Q3SYW2, Q9WUN2, O75594, O95786, P08953, P01024, P58682 700 32 5680 3.8035714285714284 0.02335216213493574 0.011745054216744988 0.015928883512450476 GOTERM_BP_FAT GO:0006952~defense response 26 2.850877192982456 1.1530485350502172E-5 Q9UGM3, P26262, Q9UHD2, P54319, P09917, Q2HJ57, Q00685, O43196, Q8IWY4, Q29041, Q9UDY8, Q3SYW2, O75594, P09960, Q9H0E2, P01024, P42768, Q15485, O70497, Q689D1, Q9Z2F6, Q6P4R8, Q9WUN2, O95786, P08953, P58682 700 83 5680 2.5418244406196213 0.029892522822571266 0.010065141456729099 0.020458014382318535 GOTERM_BP_FAT GO:0050778~positive regulation of immune response 13 1.425438596491228 1.2422483647288984E-5 Q15485, O70497, Q00685, Q29041, Q689D1, Q9UDY8, Q3SYW2, P10809, Q9WUN2, P51617, P01024, P58682, Q4JIM4 700 25 5680 4.219428571428572 0.032167438228759115 0.008140728344190884 0.022040481693264002 GOTERM_BP_FAT GO:0031396~regulation of protein ubiquitination 12 1.3157894736842104 1.7725334295725325E-5 Q8WU17, O43242, P49615, P25788, P28072, P60901, Q6PEC4, P55036, Q5U2S1, Q9BZE4, O75832, O00232 700 22 5680 4.425974025974027 0.04558194749011102 0.009287302775757178 0.03144762139538626 GOTERM_BP_FAT GO:0006955~immune response 25 2.7412280701754383 3.652527038790537E-5 Q9UGM3, Q9UHD2, Q00685, Q29041, P40792, Q9UDY8, Q9UH65, Q3SYW2, O75594, Q9H0E2, P01024, Q9BUD6, P42768, Q15485, O70497, Q689D1, Q9Z2F6, P09215, Q9WUN2, P10809, O95786, P08953, Q2I6J1, P58682, Q4JIM4 700 83 5680 2.4440619621342514 0.0916597695022422 0.01589503043170848 0.06479156276466558 GOTERM_BP_FAT GO:0051248~negative regulation of protein metabolic process 16 1.7543859649122806 3.9906884383559516E-5 P25788, O43242, P60901, P70541, P21333, Q9BZE4, P09215, P49615, P28072, P27169, P55036, Q4JIM4, O75832, P48809, Q29611, O00232 700 40 5680 3.2457142857142856 0.0997088028147719 0.01489326959340398 0.07078814698031621 GOTERM_BP_FAT GO:0002684~positive regulation of immune system process 15 1.644736842105263 6.431474055384353E-5 Q15485, Q00685, O70497, Q29041, Q689D1, Q9UDY8, Q29RN6, Q3SYW2, P10809, Q9WUN2, P51617, A7MB54, P01024, P58682, Q4JIM4 700 37 5680 3.2895752895752897 0.15572908018684184 0.02093792322045096 0.11406029928391348 GOTERM_BP_FAT GO:0031400~negative regulation of protein modification process 11 1.2061403508771928 7.372317770702441E-5 P09215, O43242, P49615, P25788, P28072, P60901, P55036, Q9BZE4, Q4JIM4, O75832, O00232 700 21 5680 4.250340136054422 0.1763804416139726 0.021329957518478992 0.13073558887951586
!wc -l chart_EA61531C2B4A1407365629460.txt
261 chart_EA61531C2B4A1407365629460.txt
pwd
u'/Users/sr320/Dropbox/Steven/eimd/data'
!wget http://david.abcc.ncifcrf.gov/data/download/chart_9BC7851772AA1407535638846.txt
--2014-08-08 15:08:31-- http://david.abcc.ncifcrf.gov/data/download/chart_9BC7851772AA1407535638846.txt Resolving david.abcc.ncifcrf.gov... 129.43.1.164 Connecting to david.abcc.ncifcrf.gov|129.43.1.164|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 16944 (17K) [text/plain] Saving to: `chart_9BC7851772AA1407535638846.txt' 100%[======================================>] 16,944 105K/s in 0.2s 2014-08-08 15:08:32 (105 KB/s) - `chart_9BC7851772AA1407535638846.txt' saved [16944/16944]
!wget http://david.abcc.ncifcrf.gov/data/download/chart_9BC7851772AA1407536148549.txt
--2014-08-08 15:16:34-- http://david.abcc.ncifcrf.gov/data/download/chart_9BC7851772AA1407536148549.txt Resolving david.abcc.ncifcrf.gov... 129.43.1.164 Connecting to david.abcc.ncifcrf.gov|129.43.1.164|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1844 (1.8K) [text/plain] Saving to: `chart_9BC7851772AA1407536148549.txt' 100%[======================================>] 1,844 --.-K/s in 0s 2014-08-08 15:16:35 (87.9 MB/s) - `chart_9BC7851772AA1407536148549.txt' saved [1844/1844]
!wget http://david.abcc.ncifcrf.gov/data/download/chart_9BC7851772AA1407536297603.txt
--2014-08-08 15:18:59-- http://david.abcc.ncifcrf.gov/data/download/chart_9BC7851772AA1407536297603.txt Resolving david.abcc.ncifcrf.gov... 129.43.1.164 Connecting to david.abcc.ncifcrf.gov|129.43.1.164|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 3943 (3.9K) [text/plain] Saving to: `chart_9BC7851772AA1407536297603.txt' 100%[======================================>] 3,943 --.-K/s in 0.07s 2014-08-08 15:18:59 (52.8 KB/s) - `chart_9BC7851772AA1407536297603.txt' saved [3943/3943]
!curl -O http://david.abcc.ncifcrf.gov/data/download/chart_9BC7851772AA1407536827905.txt
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 2702 100 2702 0 0 4239 0 --:--:-- --:--:-- --:--:-- 17101
!curl -O http://david.abcc.ncifcrf.gov/data/download/chart_9BC7851772AA1407538680797.txt
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1660 100 1660 0 0 2444 0 --:--:-- --:--:-- --:--:-- 10641
!curl -O http://david.abcc.ncifcrf.gov/data/download/chart_9BC7851772AA1407539667252.txt
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 75765 100 75765 0 0 76504 0 --:--:-- --:--:-- --:--:-- 128k
!curl -O http://david.abcc.ncifcrf.gov/data/download/chart_9BC7851772AA1407539729186.txt
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 11204 100 11204 0 0 15468 0 --:--:-- --:--:-- --:--:-- 36258
!curl -O http://david.abcc.ncifcrf.gov/data/download/chart_9BC7851772AA1407539807701.txt
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 14210 100 14210 0 0 36171 0 --:--:-- --:--:-- --:--:-- 45987
!curl -O http://david.abcc.ncifcrf.gov/data/download/list_9BC7851772AA1407539915541.txt
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 57709 100 57709 0 0 53887 0 0:00:01 0:00:01 --:--:-- 87042
!head list_9BC7851772AA1407539915541.txt
UNIPROT_ACCESSION Name Species Q62760 translocase of outer mitochondrial membrane 20 homolog (yeast) Rattus norvegicus Q6PC91 similar to basic transcription factor 3-like 4; basic transcription factor 3-like 4 Danio rerio Q5XIR6 IQ motif containing D Rattus norvegicus Q29RV1 protein disulfide isomerase family A, member 4 Bos taurus P19440 gamma-glutamyltransferase light chain 3; gamma-glutamyltransferase 4 pseudogene; gamma-glutamyltransferase 2; gamma-glutamyltransferase 1; gamma-glutamyltransferase light chain 5 pseudogene Homo sapiens P50169 retinol dehydrogenase 7 Rattus norvegicus Q6P8E9 NHP2-like protein 1 Xenopus (Silurana) tropicalis P96202 Rv2933; MRA_2959 Mycobacterium tuberculosis P40937 replication factor C (activator 1) 5, 36.5kDa Homo sapiens
!curl -O http://david.abcc.ncifcrf.gov/data/download/t2t_9BC7851772AA1407540291668.txt
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 539k 100 539k 0 0 116k 0 0:00:04 0:00:04 --:--:-- 134k
!head t2t_9BC7851772AA1407540291668.txt
Annotation Cluster 1 Enrichment Score: 10.783523294686532 Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR SP_PIR_KEYWORDS glycoprotein 179 19.62719298245614 3.1911856757633745E-17 Q5MB13, P98156, Q5RFU0, Q9GL24, P0C6B8, Q8TEY5, Q9HBY0, Q8IWY4, Q64319, Q9NYB5, Q91Z92, Q9VCA2, Q8BGT0, Q5QQ56, Q99M80, Q8BYI9, A0JP86, P10079, P55115, Q62867, Q9W735, P28863, Q689D1, P33945, Q99N02, A2BGL3, P16393, Q8SQC1, P70549, Q6DEL2, Q8IUX8, B0FYY4, Q8BGC9, A7Y2W8, O35887, O15118, Q5RB37, Q09225, Q761V0, Q6FHJ7, Q6TUG0, Q32KH9, O15335, Q32KH5, Q9GZR5, Q96RW7, Q6Y1H2, Q00685, Q29041, Q12719, O76082, Q2IBC0, Q5UQP2, Q5RBP9, P49013, Q06805, Q06806, Q9NJ15, P91660, Q9DC23, Q8JIY1, P97717, Q5E985, Q969X5, Q5R9A7, Q1HG43, Q32KI9, Q9BVH7, P46023, Q15485, P05689, P41234, Q5RD64, P41233, Q90744, Q61469, O14522, P27169, P08953, Q5HZQ9, Q95R48, Q9HCB6, P13280, Q9JME2, P58682, Q8N695, Q00945, Q9UM22, Q9UKP5, Q9C0A0, A5D6U8, P06027, P11584, Q9ULZ9, P97280, P16444, Q8C172, O15072, Q6GQ29, Q7TMS5, O75594, A2AVA0, P23978, P23975, Q06496, B7ZCC9, Q8VEL2, Q5RDQ8, P01024, P56489, P23471, Q49B93, Q17QJ5, P19440, Q6DCX5, Q9U539, Q28727, Q9WTR0, Q9GZU5, Q8K1T0, Q90YK5, O94985, O77656, P21836, P35822, Q08E66, Q9DBB9, Q5R4J5, Q8TDX6, Q6NY73, Q8TCT9, Q21974, Q9HAR2, Q6DNG6, Q29611, O35464, P26262, Q9UGM3, Q3V1H3, Q6IP59, P08582, Q6UWV6, Q6UWM7, Q9NZR2, Q9Z2J0, Q8IZJ3, Q7Z2H8, Q3ZMH1, Q61824, Q3SYW2, Q9VTK2, Q9ESG5, O54715, Q00651, Q8BMN4, Q29499, Q24322, P30937, Q9BUD6, Q6PCJ9, Q5MJS3, P28648, O70497, Q866N2, A2VDP6, Q9VGY6, Q5BL72, Q7SIB2, Q5PRC1, Q94887, Q96MC6, Q6P5E4, P54802, P41148, A2RSQ0, Q9QYM0, Q80V70, Q9PWA0, Q9VBW3 882 828 7380 1.8088829734792469 1.5604897954482902E-14 1.5604897954482902E-14 4.5810645999961623E-14 UP_SEQ_FEATURE glycosylation site:N-linked (GlcNAc...) 171 18.75 2.0249299138907436E-15 Q5MB13, P98156, Q5RFU0, Q9GL24, P0C6B8, Q8TEY5, Q9HBY0, Q8IWY4, Q64319, Q9NYB5, Q91Z92, Q9VCA2, Q8BGT0, Q5QQ56, Q99M80, Q8BYI9, A0JP86, P10079, P55115, Q62867, Q9W735, P28863, Q689D1, P33945, Q99N02, A2BGL3, P16393, Q8SQC1, P70549, Q6DEL2, Q8IUX8, B0FYY4, Q8BGC9, A7Y2W8, O35887, O15118, Q5RB37, Q09225, Q761V0, Q6FHJ7, Q6TUG0, Q32KH9, Q32KH5, Q9GZR5, Q96RW7, Q6Y1H2, Q00685, Q29041, Q12719, O76082, Q2IBC0, Q5RBP9, P49013, Q06805, Q06806, Q9NJ15, P91660, Q9DC23, Q8JIY1, P97717, Q969X5, Q5E985, Q5R9A7, Q1HG43, Q32KI9, Q9BVH7, P46023, Q15485, P05689, P41234, Q5RD64, P41233, Q90744, Q61469, O14522, P27169, P08953, Q5HZQ9, Q95R48, Q9HCB6, Q9JME2, P58682, Q8N695, Q00945, Q9UM22, Q9UKP5, Q9C0A0, A5D6U8, P11584, Q9ULZ9, P97280, P16444, Q8C172, O15072, Q6GQ29, Q7TMS5, O75594, A2AVA0, P23978, P23975, Q06496, B7ZCC9, Q8VEL2, Q5RDQ8, P01024, P56489, P23471, Q49B93, Q17QJ5, P19440, Q6DCX5, Q9U539, Q28727, Q9WTR0, Q9GZU5, Q8K1T0, Q90YK5, O94985, O77656, P21836, P35822, Q08E66, Q9DBB9, Q5R4J5, Q8TDX6, Q6NY73, Q8TCT9, Q21974, Q9HAR2, Q6DNG6, Q29611, O35464, P26262, Q9UGM3, Q3V1H3, Q6IP59, P08582, Q6UWV6, Q6UWM7, Q9NZR2, Q9Z2J0, Q8IZJ3, Q7Z2H8, Q3ZMH1, Q61824, Q3SYW2, Q9VTK2, Q9ESG5, O54715, Q8BMN4, Q00651, Q29499, Q24322, P30937, Q6PCJ9, Q5MJS3, P28648, O70497, A2VDP6, Q9VGY6, Q5BL72, Q5PRC1, Q94887, Q96MC6, Q6P5E4, P54802, P41148, A2RSQ0, Q9QYM0, Q80V70, Q9VBW3 892 796 7381 1.7775973477251727 4.696243394164412E-12 4.696243394164412E-12 3.497202527569243E-12 SP_PIR_KEYWORDS disulfide bond 102 11.18421052631579 4.893175620619848E-11 Q5MB13, P98156, Q9GL24, P0C6B8, Q8IWY4, Q64319, Q99M80, Q5QQ56, Q8BYI9, P10079, A0JP86, P55115, P28863, Q689D1, Q8IUX8, B0FYY4, Q6FHJ7, Q6TUG0, O15335, Q96RW7, Q00685, Q12719, Q29041, Q2IBC0, Q9UDY8, P00687, P49013, Q06805, Q06806, Q8JIY1, P97717, Q5E985, Q9BVH7, P46023, Q15485, P05689, Q5RD64, Q90744, P41233, O14522, P27169, P08953, Q9HCB6, Q00945, Q9UKP5, Q9C0A0, P06027, Q9ULZ9, P11584, P80147, P16444, O15072, Q3T0K2, O75594, Q7TMS5, A2AVA0, Q06496, P01024, P56489, P25325, Q9WTR6, A0JM12, Q29RV1, Q9WTR0, Q8K1T0, P82251, P35822, P21836, O77656, Q08E66, Q9R0S2, Q6NY73, O88281, Q6DNG6, Q9HAR2, Q69BJ8, O35464, Q9UGM3, P26262, Q3V1H3, P49585, P08582, Q9NZR2, Q7Z2H8, Q61824, Q3SYW2, Q9ESG5, Q8BMN4, Q00651, Q24322, Q29499, P30937, Q9BUD6, Q6PCJ9, O70497, Q866N2, P08594, Q5BL72, Q7SIB2, Q94887, P41148, Q80V70 882 448 7380 1.9050655976676385 2.3927624215325238E-8 1.196381216317377E-8 7.024332226990282E-8 SP_PIR_KEYWORDS signal 129 14.144736842105262 6.168913185383689E-11 P98156, Q5RFU0, Q9GL24, P0C6B8, Q8IWY4, Q5BLE8, Q8BGT0, Q99M80, Q8BYI9, P10079, A0JP86, P55115, Q62867, Q566I3, P28863, Q689D1, P33945, Q6PHY8, P70549, Q8IUX8, B0FYY4, Q9DCT5, Q8BGC9, O35887, O15118, Q5RB37, Q09225, Q6FHJ7, Q96PB1, Q6TUG0, Q32KH9, O15335, Q32KH5, Q96RW7, Q00685, Q29041, Q12719, Q2IBC0, Q5RBP9, P00687, P49013, Q06805, Q06806, Q9NJ15, Q13217, Q9DC23, Q8JIY1, Q5E985, Q32KI9, P46023, Q15485, P05689, Q5RD64, O14522, P27169, P08953, Q9HCB6, P81134, P58682, Q00945, Q9UM22, Q9UKP5, Q9C0A0, A5D6U8, Q9ULZ9, P11584, Q91WM2, P97280, P16444, Q6GQ29, O15072, O75594, A2AVA0, B7ZCC9, Q5RDQ8, P01024, P23471, A0JM12, P28622, Q9WTR0, Q29RV1, Q9GZU5, Q90YK5, O94985, P21836, O77656, P35822, Q08E66, Q9DBB9, Q9R0S2, Q6NY73, O88281, Q9HAR2, O35464, Q9UGM3, P26262, Q3V1H3, Q90593, Q0VA61, P08582, Q6UWV6, Q6UWM7, Q9NZR2, Q8IZJ3, Q61824, Q3SYW2, Q9ESG5, O54715, Q92544, Q00651, Q29499, Q24322, Q9BUD6, Q6PCJ9, P09848, Q5MJS3, O70497, Q866N2, P08594, A2VDP6, Q9VGY6, Q5BL72, Q5PRC1, Q94887, Q6P5E4, P54802, P41148, Q80V70, Q9VBW3 882 620 7380 1.740947992100066 3.016596861193932E-8 1.0055323018676177E-8 8.855697286591635E-8 UP_SEQ_FEATURE signal peptide 129 14.144736842105262 1.3591537204927445E-10 P98156, Q5RFU0, Q9GL24, P0C6B8, Q8IWY4, Q5BLE8, Q8BGT0, Q99M80, Q8BYI9, P10079, A0JP86, P55115, Q62867, Q566I3, P28863, Q689D1, P33945, Q6PHY8, P70549, Q8IUX8, B0FYY4, Q9DCT5, Q8BGC9, O35887, O15118, Q5RB37, Q09225, Q6FHJ7, Q96PB1, Q6TUG0, Q32KH9, O15335, Q32KH5, Q96RW7, Q00685, Q29041, Q12719, Q2IBC0, Q5RBP9, P00687, P49013, Q06805, Q06806, Q9NJ15, Q13217, Q9DC23, Q8JIY1, Q5E985, Q32KI9, P46023, Q15485, P05689, Q5RD64, O14522, P27169, P08953, Q9HCB6, P81134, P58682, Q00945, Q9UM22, Q9UKP5, Q9C0A0, A5D6U8, Q9ULZ9, P11584, Q91WM2, P97280, P16444, Q6GQ29, O15072, O75594, A2AVA0, B7ZCC9, Q5RDQ8, P01024, P23471, A0JM12, P28622, Q9WTR0, Q29RV1, Q9GZU5, Q90YK5, O94985, P21836, O77656, P35822, Q08E66, Q9DBB9, Q9R0S2, Q6NY73, O88281, Q9HAR2, O35464, Q9UGM3, P26262, Q3V1H3, Q90593, Q0VA61, P08582, Q6UWV6, Q6UWM7, Q9NZR2, Q8IZJ3, Q61824, Q3SYW2, Q9ESG5, O54715, Q92544, Q00651, Q29499, Q24322, Q9BUD6, Q6PCJ9, P09848, Q5MJS3, O70497, Q866N2, P08594, A2VDP6, Q9VGY6, Q5BL72, Q5PRC1, Q94887, Q6P5E4, P54802, P41148, Q80V70, Q9VBW3 892 620 7381 1.7216638941125415 3.1940111566708396E-7 1.597005705455956E-7 2.3808145455106455E-7 SP_PIR_KEYWORDS Secreted 65 7.12719298245614 2.5912723422829477E-10 Q00945, Q9UM22, Q9UKP5, P0C6B8, A5D6U8, Q8IWY4, P06027, Q9ULZ9, P97280, O15072, Q6GQ29, O75594, A2AVA0, Q8BYI9, A0JP86, P10079, P01024, P55115, Q62867, P28622, P28863, P33945, Q9GZU5, Q90YK5, O77656, P21836, Q8IUX8, Q08E66, Q9DCT5, Q9DBB9, Q9R0S2, Q8BGC9, Q6NY73, O35887, Q5RB37, O88281, Q6FHJ7, O15335, Q9UGM3, P26262, Q96RW7, Q00685, Q12719, Q29041, Q8IZJ3, Q3SYW2, Q8BHR2, P00687, P49013, Q9NJ15, Q29499, Q9DC23, Q9BUD6, Q5E985, Q5MJS3, Q32KI9, Q15485, O70497, Q866N2, P08594, A2VDP6, Q7SIB2, P27169, Q9HCB6, Q80V70 882 242 7380 2.2474278967785457 1.267132295756923E-7 3.1678308864968585E-8 3.719867525120435E-7 UP_SEQ_FEATURE disulfide bond 91 9.978070175438598 3.540563571267061E-9 Q00945, Q5MB13, P98156, Q9GL24, Q9UKP5, P0C6B8, Q9C0A0, Q8IWY4, P06027, P11584, Q9ULZ9, P80147, P16444, O15072, Q3T0K2, O75594, Q7TMS5, Q99M80, A2AVA0, Q06496, Q8BYI9, A0JP86, P10079, P01024, P55115, P56489, A0JM12, P28863, Q29RV1, Q9WTR0, Q689D1, Q8K1T0, P35822, P21836, O77656, Q8IUX8, Q08E66, B0FYY4, Q9R0S2, Q6NY73, O88281, Q9HAR2, Q6DNG6, Q6FHJ7, Q69BJ8, O35464, O15335, Q9UGM3, P26262, Q3V1H3, P49585, P08582, Q96RW7, Q00685, Q12719, Q9NZR2, Q9UDY8, Q7Z2H8, Q61824, Q3SYW2, P00687, Q9ESG5, P49013, Q00651, Q8BMN4, Q06805, Q06806, Q24322, Q29499, P30937, Q9BUD6, Q8JIY1, P97717, Q5E985, Q6PCJ9, Q9BVH7, P46023, P05689, Q5RD64, Q866N2, Q90744, P08594, P41233, Q5BL72, O14522, Q7SIB2, Q94887, P27169, Q9HCB6, P41148, Q80V70 892 408 7381 1.8455744966147896 8.320289908048117E-6 2.773437661307554E-6 6.201965185859137E-6 GOTERM_CC_FAT GO:0005576~extracellular region 73 8.00438596491228 2.2171653159552866E-7 Q9UM22, Q00945, P98156, Q9UKP5, P0C6B8, Q8IWY4, A5D6U8, P06027, Q9ULZ9, P97280, O15072, Q6GQ29, O75594, A2AVA0, Q8BYI9, A0JP86, P10079, P01024, P55115, P23471, Q62867, P28622, P28863, P21333, Q9WTR0, P33945, Q9GZU5, Q90YK5, O77656, P21836, Q8IUX8, Q08E66, Q9DCT5, Q9DBB9, P10809, Q9R0S2, Q8BGC9, Q6NY73, O35887, Q5RB37, O88281, Q6FHJ7, O15335, Q9UGM3, P26262, Q96RW7, P08582, Q00685, Q12719, Q29041, Q8IZJ3, Q61824, Q3SYW2, Q8BHR2, P00687, P49013, Q9NJ15, Q29499, Q9DC23, Q9BUD6, Q5E985, Q5MJS3, Q32KI9, Q15485, O70497, Q866N2, P08594, A2VDP6, Q99943, Q7SIB2, P27169, Q9HCB6, Q80V70 602 285 4225 1.7976627615550502 9.04562634979067E-5 9.04562634979067E-5 3.10142167947447E-4
Using Benjamini < 0.5
#with bejamini less than 0.5 - 23 GO terms
pwd
u'/Users/sr320/Dropbox/Steven/eimd/data'
!head 08014REVIGO_treemap.csv
!head 0814REVIGO_treemap.r