Bicluster 232 (zzz

[+] Show/hide bicluster #232 rows and columns.

bicluster 232 Mycobacterium tuberculosis H37Rv 16x11

RV0651
RV0701
RV0703
RV0706
RV0707
RV0708
RV0709
RV0710
RV0714
RV0717
RV0720
RV0721
RV0722
RV0723
RV2725C
RV3028C

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.KCN...2hr.hypoxia.rep.3
4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.01.mM.DETA.NO.rep.3
4615:::AA_30uM_2h_05
4615:::AA_30uM_2h_06
4615:::OA_50uM_2h_10
4615:::Rv.MT96_100703_01
4799:::H37Rv.O2.depleted..ctrl.vs.1ug.ml.Isoniazid.for.2hrs.rep.3
Provvedi_Microbiology2009:::H37Rv.Control.vs.400.ug.ml.vancomycin.for.1.hr.DS.rep.2
Rohde_CellHostMicrobe2007:::CDC1551.ctrl.vs.pH.5.5.7H9.broth.for.2.hr
Rohde_CellHostMicrobe2007:::CDC1551.ctrl.vs.pH.6.5.7H9.broth.for.2.hr

[+] Show/hide bicluster #232 rows (genes).

bicluster 232 genes Mycobacterium tuberculosis H37Rv 16

RV0651
RV0701
RV0703
RV0706
RV0707
RV0708
RV0709
RV0710
RV0714
RV0717
RV0720
RV0721
RV0722
RV0723
RV2725C
RV3028C

[+] Show/hide bicluster #232 rows (short gene names).

bicluster 232 short names Mycobacterium tuberculosis H37Rv 16 short_name

RV0651	rplJ
RV0701	rplC
RV0703	rplW
RV0706	rplV
RV0707	rpsC
RV0708	rplP
RV0709	rpmC
RV0710	rpsQ
RV0714	rplN
RV0717	rpsN
RV0720	rplR
RV0721	rpsE
RV0722	rpmD
RV0723	rplO
RV2725C	hflX
RV3028C	fixB

[+] Show/hide bicluster #232 rows (long gene names).

bicluster 232 long names Mycobacterium tuberculosis H37Rv 16 long_name

RV0651	50S ribosomal protein L10
RV0701	50S ribosomal protein L3
RV0703	50S ribosomal protein L23
RV0706	50S ribosomal protein L22
RV0707	30S ribosomal protein S3
RV0708	50S ribosomal protein L16
RV0709	50S ribosomal protein L29
RV0710	30S ribosomal protein S17
RV0714	50S ribosomal protein L14
RV0717	30S ribosomal protein S14
RV0720	50S ribosomal protein L18
RV0721	30S ribosomal protein S5
RV0722	50S ribosomal protein L30
RV0723	50S ribosomal protein L15
RV2725C	PROBABLE GTP-BINDING PROTEIN HFLX
RV3028C	PROBABLE ELECTRON TRANSFER FLAVOPROTEIN (ALPHA-SUBUNIT) FIXB (ALPHA-ETF) (ELECTRON TRANSFER FLAVOPROTEIN LARGE SUBUNIT) (ETFLS)

[+] Show/hide bicluster #232 rows (NCBI RefSeq gene IDs).

bicluster 232 NCBI RefSeq IDs Mycobacterium tuberculosis H37Rv 30

NP_215165
NP_215165.1
NP_215215
NP_215215.1
NP_215217
NP_215217.1
NP_215220
NP_215220.1
NP_215221
NP_215221.1
NP_215222
NP_215222.1
NP_215223
NP_215223.1
NP_215224
NP_215224.1
NP_215228
NP_215228.1
NP_215234
NP_215234.1
NP_215235
NP_215235.1
NP_215236
NP_215236.1
NP_215237
NP_215237.1
NP_217241
NP_217241.1
NP_217544
NP_217544.1

[+] Show/hide bicluster #232 gene upstream sequences.

bicluster 232 upstream sequences Mycobacterium tuberculosis H37Rv 16 upstream

RV0651	CGCAGGAGGACGAGGCAGCACCGCCGGCGCGCGCCGGCCTAGTTCCACGCCCCGACCGCTTCCTGCGTCGGGGCGTTCGTCGTTCCCGGGTGGTCGCAGACGGCACGTCGTACCCCGACTGCCACCAGACTTGCACCGTCAGGAGGTATGCATGGCCAGGGCTGACAAGG
RV0701	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV0703	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV0707	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV0708	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV0709	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV0710	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV0714	TCAGGGGTTGCCGTGAGCAGACCTCGGCCGGCGCGCATAAGCTTTGCTTGGTCGGCCCCGCGTGCCCGTCGGCGACAAAGACCGCGCACGTCAGGGATGGTCCTGGCTGGCTCCTCCTACCGTGCACACGTCAACCAGGTCAGGAGATCTAGTGATTCAGCAGGAATCGC
RV0720	TCAGGGGTTGCCGTGAGCAGACCTCGGCCGGCGCGCATAAGCTTTGCTTGGTCGGCCCCGCGTGCCCGTCGGCGACAAAGACCGCGCACGTCAGGGATGGTCCTGGCTGGCTCCTCCTACCGTGCACACGTCAACCAGGTCAGGAGATCTAGTGATTCAGCAGGAATCGC
RV0721	TCAGGGGTTGCCGTGAGCAGACCTCGGCCGGCGCGCATAAGCTTTGCTTGGTCGGCCCCGCGTGCCCGTCGGCGACAAAGACCGCGCACGTCAGGGATGGTCCTGGCTGGCTCCTCCTACCGTGCACACGTCAACCAGGTCAGGAGATCTAGTGATTCAGCAGGAATCGC
RV0722	TCAGGGGTTGCCGTGAGCAGACCTCGGCCGGCGCGCATAAGCTTTGCTTGGTCGGCCCCGCGTGCCCGTCGGCGACAAAGACCGCGCACGTCAGGGATGGTCCTGGCTGGCTCCTCCTACCGTGCACACGTCAACCAGGTCAGGAGATCTAGTGATTCAGCAGGAATCGC
RV0723	TCAGGGGTTGCCGTGAGCAGACCTCGGCCGGCGCGCATAAGCTTTGCTTGGTCGGCCCCGCGTGCCCGTCGGCGACAAAGACCGCGCACGTCAGGGATGGTCCTGGCTGGCTCCTCCTACCGTGCACACGTCAACCAGGTCAGGAGATCTAGTGATTCAGCAGGAATCGC
RV2725C	GAACGCTCACCGTGCACGTGCCGGGCGGAGAGGTCGTGGTTACCGTCACCGATGCCACCAGCTTCCTGCGTGGGCCGTCAGTGTTGGTGGCCCGCGGAGATCTCGCTGACGATTGGTGGAACGCGATGGGGTGATCCCAGGCAGCGGCTTATGCCGGCAAATTCAGATGC
RV3028C	CGTGGGAACCTGCTCTACCACCCGCTATGGTGTGAGGGCGCACCACGCGAACTTACCGAATAGTAATATCGCTGTGCGGTTGCAAAACGTGTGACCGAGGTTCCGCAGTCGAGCGCTGCGGGCCGCCTTCGAGGAGGACGAACCACAGTCATGACGAACATCGTGGTCCT
RV0706	CCCGAGCGCGGGGCCGGTGGACCTACGACAGGTAAACAGCGGCGCAGTATTCGGCGCAACGCTAGATCGGTCCAGAAGGACCGGGTCGATCGGCGCGCCGGGGAGCACCGGACCCGGATACGGGCTCGAGTGGGAGTGAGGTAGGAGAAGCGTGGCGGGACAGAAGATCC
RV0717	TCAGGGGTTGCCGTGAGCAGACCTCGGCCGGCGCGCATAAGCTTTGCTTGGTCGGCCCCGCGTGCCCGTCGGCGACAAAGACCGCGCACGTCAGGGATGGTCCTGGCTGGCTCCTCCTACCGTGCACACGTCAACCAGGTCAGGAGATCTAGTGATTCAGCAGGAATCGC

[+] Show/hide bicluster #232 columns (arrays; conditions).

bicluster 232 arrays Mycobacterium tuberculosis H37Rv 11

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.KCN...2hr.hypoxia.rep.3
4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.01.mM.DETA.NO.rep.3
4615:::AA_30uM_2h_05
4615:::AA_30uM_2h_06
4615:::OA_50uM_2h_10
4615:::Rv.MT96_100703_01
4799:::H37Rv.O2.depleted..ctrl.vs.1ug.ml.Isoniazid.for.2hrs.rep.3
Provvedi_Microbiology2009:::H37Rv.Control.vs.400.ug.ml.vancomycin.for.1.hr.DS.rep.2
Rohde_CellHostMicrobe2007:::CDC1551.ctrl.vs.pH.5.5.7H9.broth.for.2.hr
Rohde_CellHostMicrobe2007:::CDC1551.ctrl.vs.pH.6.5.7H9.broth.for.2.hr

[+] Show/hide bicluster #232 ratios.

bicluster 232 ratios Mycobacterium tuberculosis H37Rv 16x11

GENES 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.KCN...2hr.hypoxia.rep.3 4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.01.mM.DETA.NO.rep.3 4615:::AA_30uM_2h_05 4615:::AA_30uM_2h_06 4615:::OA_50uM_2h_10 4615:::Rv.MT96_100703_01 4799:::H37Rv.O2.depleted..ctrl.vs.1ug.ml.Isoniazid.for.2hrs.rep.3 Provvedi_Microbiology2009:::H37Rv.Control.vs.400.ug.ml.vancomycin.for.1.hr.DS.rep.2 Rohde_CellHostMicrobe2007:::CDC1551.ctrl.vs.pH.5.5.7H9.broth.for.2.hr Rohde_CellHostMicrobe2007:::CDC1551.ctrl.vs.pH.6.5.7H9.broth.for.2.hr RV0651 -0.698579715172188 -3.6374323100345 1.78258272147386 0.149886835439243 0.911811582255397 1.53634006325224 0.936792721495271 1.42229573193978 0.524737398022541 -7.354 -0.684 RV0701 -0.644029886467975 NA 0.435155328694578 0.727915770128206 1.1553158553411 2.19710356304752 0.674490759476595 3.42006490981662 0.0561656442845924 -5.56798788549411 -0.252061027466779 RV0703 -2.772906455626 -2.81037816448581 0.474641645557604 0.5745662025171 0.799396455675965 1.61128348097187 1.02422670883483 2.92827695577644 0.431765764372358 -5.3295 -0.966 RV0706 -2.25254461183693 -2.81249920460995 0.572680833517864 -0.189109558731756 0.718616323180672 1.28594499937594 1.38680343069954 NA 0.541192163741904 -4.3755 -0.502 RV0707 -2.95800766806603 -4.07945013562953 0.763881101093975 0.839366278459763 1.37895888604104 1.85859675944662 1.0492078480747 2.58233605056754 0.873522290422923 -4.04394586818613 -0.395398520798284 RV0708 -3.35470404055464 -3.53220160883796 0.85198832775991 0.762467815060499 1.46628425973173 1.59824984310758 1.21701593557733 1.49166225653478 0.630942684032971 -2.75875 0.08525 RV0709 -4.51836282961203 -3.34344344213667 0.877563246200731 0.882026377777086 1.23224273365916 1.67325592254771 NA 3.04869823283421 0.630384351401725 -3.58321061875239 -1.17786007690918 RV0710 -3.02557283536644 -2.69796303790638 1.05991405060608 1.28623819249025 1.50583983511054 2.63521971144344 1.23918069764305 2.14488061513557 1.29114437317038 -4.029 -0.651 RV0714 -1.6690788285353 -2.51505028957374 0.45728187083159 1.03326244004925 0.803648564482752 1.77950753564038 0.803648564482752 2.49496096466585 NA -4.43905376222293 -1.31909154943703 RV0717 -1.04193721799743 -2.57212520964582 0.659390220085328 0.44966050631773 1.21881663554543 1.19515029310765 NA 3.09472230818673 1.6946222625 -3.00051001600743 -0.958137568702475 RV0720 -2.06435050627685 NA 0.654051645553062 0.92970347927855 0.364589599717078 1.13022775912294 0.619802319519033 3.24350703454186 0.6508793275 -6.62375 -0.11325 RV0721 -1.49351525312675 -4.16738933533753 0.674490759476595 0.580811487327068 1.34898151895319 1.55507591768215 0.337245379738298 3.69882029390391 1.07832609506851 -5.48325 -1.66375 RV0722 -2.38665961045564 -4.60037287232755 1.15874053551107 0.7935185405607 1.09770064777564 1.36220682796254 1.42833337300926 1.54422884406484 1.16788016965638 -3.29686846602122 -0.638864552337931 RV0723 -1.10476934741856 -4.2911567283942 NA 0.571850861295374 2.02347227842979 1.75954111167807 0.395896750127567 3.99506065228445 0.135177665600008 -3.72025 0.0462499999999999 RV2725C -0.944287063267233 -2.67098340752732 0.782409280992851 0.458653716444085 1.21408336705787 3.69620936193174 1.10616484554162 1.43508672229063 -0.120895897673665 -3.36925 -0.55425 RV3028C -3.22256696194373 -3.82211430370071 0.44966050631773 -0.164065319872685 -0.565113879561472 1.31252255898148 -0.328130639745371 1.65924726831242 1.0119002225 -4.534 0.65

[+] Show/hide bicluster #232 motif PSSM #1.

bicluster 232 motif PSSM #1 Mycobacterium tuberculosis H37Rv 7x4

POSITION A C G T 1 0 0 0 1 2 0 0.8 0 0.2 3 0 1 0 0 4 0.2 0 0 0.8 5 0 1 0 0 6 0 1 0 0 7 0.2 0 0 0.8

[+] Show/hide bicluster #232 motif PSSM #2.

bicluster 232 motif PSSM #2 Mycobacterium tuberculosis H37Rv 11x4

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