Bicluster 354 (zzz

[+] Show/hide bicluster #354 rows and columns.

bicluster 354 Mycobacterium tuberculosis H37Rv 13x17

RV0315
RV0667
RV0668
RV0682
RV0683
RV0684
RV0685
RV0700
RV0701
RV0702
RV0704
RV0705
RV1649

4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.3
4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.5
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs...0.5.mM.DNO.40min.rep.2
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs...0.5.mM.DNO.40min.rep.4
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.40min.rep.3
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.8hrs.rep.3
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.8hrs.rep.4
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.1
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.2
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.3
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.1hr.rep.1
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.20min...0.05.mM.DETA.NO.40min.rep.2
4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.01.mM.DETA.NO.rep.3
4062:::MTB1254.Day.0.vs.low.Oxygen.Day.4.rep.3
4107:::X0.1mMGSNO.5ug.mLKCNvsDMSO.6h.A
4583:::X20ug.ml.KCN.vs.DMSO.6hrs
Rohde_CellHostMicrobe2007:::CDC1551.ctrl.vs.pH.5.5.7H9.broth.for.2.hr

[+] Show/hide bicluster #354 rows (genes).

bicluster 354 genes Mycobacterium tuberculosis H37Rv 13

RV0315
RV0667
RV0668
RV0682
RV0683
RV0684
RV0685
RV0700
RV0701
RV0702
RV0704
RV0705
RV1649

[+] Show/hide bicluster #354 rows (short gene names).

bicluster 354 short names Mycobacterium tuberculosis H37Rv 13 short_name

RV0315	Rv0315
RV0667	rpoB
RV0668	rpoC
RV0682	rpsL
RV0683	rpsG
RV0684	fusA1
RV0685	tuf
RV0700	rpsJ
RV0701	rplC
RV0702	rplD
RV0704	rplB
RV0705	rpsS
RV1649	pheS

[+] Show/hide bicluster #354 rows (long gene names).

bicluster 354 long names Mycobacterium tuberculosis H37Rv 13 long_name

RV0315	POSSIBLE BETA-1,3-GLUCANASE PRECURSOR
RV0667	DNA-directed RNA polymerase subunit beta
RV0668	DNA-directed RNA polymerase subunit beta'
RV0682	30S ribosomal protein S12
RV0683	30S ribosomal protein S7
RV0684	elongation factor G
RV0685	elongation factor Tu
RV0700	30S ribosomal protein S10
RV0701	50S ribosomal protein L3
RV0702	50S ribosomal protein L4
RV0704	50S ribosomal protein L2
RV0705	30S ribosomal protein S19
RV1649	phenylalanyl-tRNA synthetase subunit alpha

[+] Show/hide bicluster #354 rows (NCBI RefSeq gene IDs).

bicluster 354 NCBI RefSeq IDs Mycobacterium tuberculosis H37Rv 24

NP_214829
NP_214829.1
NP_215181
NP_215181.1
NP_215182
NP_215182.1
NP_215196
NP_215196.1
NP_215197
NP_215197.1
NP_215199
NP_215199.1
NP_215214
NP_215214.1
NP_215215
NP_215215.1
NP_215216
NP_215216.1
NP_215218
NP_215218.1
NP_215219
NP_215219.1
NP_216165
NP_216165.1

[+] Show/hide bicluster #354 gene upstream sequences.

bicluster 354 upstream sequences Mycobacterium tuberculosis H37Rv 13 upstream

RV0315	CCACGTCGGCTAGCGGCCGCTCCAGTTCCCGGATTCGCGCCTCCGGGTCATCCTCTGGGTTCATGCACAGATGCTCCCACACGACGATCATGCCGCATAGGTAGTTGCGCCCGGCGGCACCACACGATTCGGCTTGGCCTGCTATCGTCCCATGCTTATGCCTGAGATGG
RV0667	AGTTTGCGGCTCAGCGGTTTAGTTGCGTGCGTGAGATCCGGACAGATCGTTCGCCGGCCGAAACCGACAAAATTATCGCGGCGAACGGGCCCGTGGGCACCGCTCCTCTAAGGGCTCTCGTTGGTCGCATGAAGTGCTGGAAGGATGCATCTTGGCAGATTCCCGCCAGA
RV0668	AGTTTGCGGCTCAGCGGTTTAGTTGCGTGCGTGAGATCCGGACAGATCGTTCGCCGGCCGAAACCGACAAAATTATCGCGGCGAACGGGCCCGTGGGCACCGCTCCTCTAAGGGCTCTCGTTGGTCGCATGAAGTGCTGGAAGGATGCATCTTGGCAGATTCCCGCCAGA
RV0682	TGGATGCCGGGCCAATTCGCATGTCCGCGATGCCTCGGATGAGACGAATCGAGTTTGAGGCAAGCTATGCGACACACCCGGCCGCGGGTAACCGTGGCGGGGCATGGCCGACAAACAGAACGTGAAAGCGCCCAAGATAGAAAGCCGGTAGATGCCAACCATCCAGCAGC
RV0683	TGGATGCCGGGCCAATTCGCATGTCCGCGATGCCTCGGATGAGACGAATCGAGTTTGAGGCAAGCTATGCGACACACCCGGCCGCGGGTAACCGTGGCGGGGCATGGCCGACAAACAGAACGTGAAAGCGCCCAAGATAGAAAGCCGGTAGATGCCAACCATCCAGCAGC
RV0684	TGGATGCCGGGCCAATTCGCATGTCCGCGATGCCTCGGATGAGACGAATCGAGTTTGAGGCAAGCTATGCGACACACCCGGCCGCGGGTAACCGTGGCGGGGCATGGCCGACAAACAGAACGTGAAAGCGCCCAAGATAGAAAGCCGGTAGATGCCAACCATCCAGCAGC
RV0685	TGGATGCCGGGCCAATTCGCATGTCCGCGATGCCTCGGATGAGACGAATCGAGTTTGAGGCAAGCTATGCGACACACCCGGCCGCGGGTAACCGTGGCGGGGCATGGCCGACAAACAGAACGTGAAAGCGCCCAAGATAGAAAGCCGGTAGATGCCAACCATCCAGCAGC
RV0700	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV0701	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV0702	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV0704	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV0705	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV1649	GATTTGCACTTGCGTCACGCCGTTAGCGGGCAAGTCGGGTACGTCCATCAGTCCAGTTTCCGCTCCGCGACGATGCGGGCGGTCCGAATAGCCTCGTCAGCAAGGAGAGTGGCGCCGCGTGGGTGATCCCCCCCTCGAGTCGATTGTGTCGATGTTGTCGCCGGAGGCAT

[+] Show/hide bicluster #354 columns (arrays; conditions).

bicluster 354 arrays Mycobacterium tuberculosis H37Rv 17

4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.3
4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.5
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs...0.5.mM.DNO.40min.rep.2
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs...0.5.mM.DNO.40min.rep.4
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.40min.rep.3
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.8hrs.rep.3
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.8hrs.rep.4
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.1
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.2
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.3
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.1hr.rep.1
4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.20min...0.05.mM.DETA.NO.40min.rep.2
4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.01.mM.DETA.NO.rep.3
4062:::MTB1254.Day.0.vs.low.Oxygen.Day.4.rep.3
4107:::X0.1mMGSNO.5ug.mLKCNvsDMSO.6h.A
4583:::X20ug.ml.KCN.vs.DMSO.6hrs
Rohde_CellHostMicrobe2007:::CDC1551.ctrl.vs.pH.5.5.7H9.broth.for.2.hr

[+] Show/hide bicluster #354 ratios.

bicluster 354 ratios Mycobacterium tuberculosis H37Rv 13x17

GENES 4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.5 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs...0.5.mM.DNO.40min.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs...0.5.mM.DNO.40min.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.40min.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.8hrs.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.8hrs.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.1hr.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.20min...0.05.mM.DETA.NO.40min.rep.2 4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.01.mM.DETA.NO.rep.3 4062:::MTB1254.Day.0.vs.low.Oxygen.Day.4.rep.3 4107:::X0.1mMGSNO.5ug.mLKCNvsDMSO.6h.A 4583:::X20ug.ml.KCN.vs.DMSO.6hrs Rohde_CellHostMicrobe2007:::CDC1551.ctrl.vs.pH.5.5.7H9.broth.for.2.hr RV0315 0.674490759476595 0.832574531228922 -1.09604748414947 -2.06562795089707 -0.653412923242952 -2.32910090381762 -2.59257385673816 -2.43449008498584 -2.5609571023877 -2.97197490894375 -0.537484823957912 -0.8220356131121 0.548023742074734 0.621796168892486 NA NA -3.55575002224803 RV0667 0.796386679863932 0.747628311708997 -1.30834954549075 -1.93408193681241 -0.796386679863932 -1.51963580749546 -1.15394804633345 -2.15349459350961 -1.69841649073022 NA -0.601353207244193 -0.593226812551704 0.828892258633888 0.869524232096334 -2.06946028475774 -4.81954306316913 -4.1061805448955 RV0668 0.710949719448303 0.765638159405865 0 -3.28130639745371 -1.11199827913709 -4.01048559688786 -1.98701331845808 -1.78648903861368 -1.56773527878344 NA -0.0364589599717079 0.765638159405865 0.145835839886831 0.41927803967464 -1.44817133652328 -4.08373496192193 -4.91525 RV0682 0.697550272621094 0.513074167465102 -0.812847838343589 -2.11571033100778 -0.962734673782833 -0.985794186927331 -1.12415126579433 -3.43010258024422 -2.68066840304801 -3.32633477109398 -1.93123422585179 -1.81593666012929 0.697550272621094 0.939675160638333 -2.04076691328816 -3.12718443030058 -3.77525 RV0683 NA 0.867202405041337 -0.841507518966038 -1.77937086071445 -0.456084227836555 -0.713033088589544 -1.88215040501564 -2.84570863283935 -2.40889556955927 -3.26967425308178 -1.5866592151497 -1.45818478477321 0.674490759476595 0.661643316438946 -2.47313278474752 -5.19642880892532 -3.39931924959016 RV0684 0.674490759476595 0.418184270875489 -0.903817617698638 -1.68622689869149 -0.296775934169702 -1.53783893160664 -1.38945096452179 -2.76541211385404 -2.56306488601106 -4.19533252394442 -0.863348172130042 -1.02522595440442 0.930797248077702 0.795899096182383 -1.15745945144749 -5.35545663024417 -5.39775 RV0685 0.98705964801453 0.855451694945926 -2.6157080672385 -3.47115976218443 -0.032901988267151 -2.51700210243705 -1.6121974250904 -2.89537496750929 -3.66857169178733 -3.75082666245521 -0.444176841606538 -1.33253052481961 0.674490759476595 0.904804677346652 -1.48387967084851 -6.12366610577435 -4.79916101122091 RV0700 0.674490759476595 0.623903952515851 -1.37427492243356 -1.96445433697558 -0.497436935113989 -1.86328072305409 -1.23937677053824 -3.20383110751383 -2.14993929583165 -3.45676514231755 -1.44172399838122 -1.42486172939431 0.379401052205585 0.573317145555106 -1.61671830897443 -3.65018528657922 -5.69875 RV0701 NA 0.73106095220689 -0.644029886467975 -2.52390090642855 -0.704951632485216 -2.42816673411574 -1.25324734664038 -1.79283995422166 -1.9581989791256 NA -1.5404498635788 -1.14881006775368 0.435155328694578 0.522186394433493 -1.80232776712598 -4.91841049388243 -5.56798788549411 RV0702 1.03421916453078 0.48338504429156 -1.94478168982418 -3.22631413282971 -0.393452943028014 -2.19209496829893 -2.28202706956248 -3.41741984801475 -3.08017446827645 -3.9232879176222 -1.05670218984667 -1.00049462655695 0.247313278474752 0.44966050631773 -1.283708219649 -1.92711645564741 -5.5385 RV0704 0.543022221612513 0.325813332967508 -1.51474619712964 -2.38358175170966 -0.177196724947241 -2.36071765816808 -2.55506245327151 -2.17780490983545 -1.59477052452517 -3.25241730628968 -0.337245379738298 -0.623046549008041 0.725934969945149 0.737367016715939 -1.91105715185035 -5.35414346239386 -3.86125 RV0705 0.567992218506606 0.982153211167674 -2.106304476962 -3.33695428372631 -0.65082441703882 -2.86362743497081 -1.85780788136536 -3.70378259151183 -2.49679912718529 -3.99961187198402 -0.106498540969989 -0.272162938034416 0.544325876068831 0.44966050631773 -2.25242785733468 -4.7274042611103 -3.66749306714206 RV1649 -0.120114792783503 0.415781975019819 -2.06043067620933 -2.30066026177633 -0.637532361697056 -2.44849385289449 -2.67024423957173 -3.13222421181597 -2.35609785844564 NA -1.24734592505946 -0.397302776130049 0.286427582791431 0.582094765027746 -0.240889556955927 -3.67597463914744 -5.21026899242286

[+] Show/hide bicluster #354 motif PSSM #1.

bicluster 354 motif PSSM #1 Mycobacterium tuberculosis H37Rv 10x4

POSITION A C G T 1 1 0 0 0 2 0.2 0 0 0.8 3 0 1 0 0 4 0.2 0.4 0.2 0.2 5 0.2 0 0.6 0.2 6 0 0 0 1 7 0 0.8 0.2 0 8 0 1 0 0 9 1 0 0 0 10 0 0 0.8 0.2

[+] Show/hide bicluster #354 motif PSSM #2.

bicluster 354 motif PSSM #2 Mycobacterium tuberculosis H37Rv 15x4

POSITION A C G T 1 0.6 0 0.4 0 2 0 0.6 0.4 0 3 0 0 0.2 0.8 4 0.8 0 0 0.2 5 0 0 0 1 6 0 0 0.4 0.6 7 0 1 0 0 8 0 0 1 0 9 0.2 0 0.8 0 10 0.2 0.8 0 0 11 0.2 0.2 0.2 0.4 12 0 0.8 0 0.2 13 0.6 0 0.4 0 14 0.2 0.4 0.4 0 15 0 1 0 0