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Coexpression cluster:C175: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;22:4.94189839572193:4.52899345798051e-10:4.40823436866753e-08!BHLHE40#8553;10:4.48718135469774:8.36338657560895e-05:0.00125587883618983!BRCA1#672;30:6.05526919296713:6.48206509114599e-16:1.23536568623028e-13!CCNT2#905;61:3.86508296194721:1.48055951119461e-24:4.62958547274412e-22!CEBPB#1051;33:2.63047871652219:9.03368834232657e-08:5.33938526759618e-06!CHD2#1106;37:3.82728844862324:1.91838667119907e-13:2.91212769699651e-11!CTCF#10664;35:1.87608973057626:8.15192580369663e-05:0.00123459828743079!CTCFL#140690;13:2.56704166666667:0.00163419287879483:0.0102273172380425!E2F1#1869;63:3.09165520537397:2.53989391911509e-20:6.54972792638174e-18!E2F4#1874;26:3.29369568197395:4.37523793755356e-08:2.87026052110651e-06!E2F6#1876;53:2.65909253779961:2.29988462341672e-13:3.45608129762617e-11!EBF1#1879;24:2.13755204317656:0.000239502796000365:0.00260692365935197!EGR1#1958;63:3.14255282973039:1.05354879233456e-20:2.76461262117158e-18!ELF1#1997;71:3.02324955075335:1.23175375566203e-23:3.73962588626706e-21!ELK4#2005;20:3.24713633169361:2.68981593024684e-06:9.4142656145794e-05!EP300#2033;32:2.16766135239142:1.08405238420193e-05:0.000281006073352358!ETS1#2113;38:3.69692915043689:2.31101688740571e-13:3.46782029746788e-11!FOS#2353;22:1.97955016795677:0.00129031842800045:0.00864896773647002!FOSL1#8061;7:2.77995058014611:0.0134267295063494:0.0474366294412784!FOSL2#2355;23:3.89394613904919:1.55161625843908e-08:1.13718772221136e-06!FOXA1#3169;28:3.10279752982793:4.06103716942618e-08:2.68097762918901e-06!GABPB1#2553;48:3.39248824136744:6.77337332062742e-16:1.28853248858471e-13!GATA1#2623;18:2.44085546588408:0.00035665791529376:0.00356722811869038!GTF2B#2959;8:2.55550639474594:0.0134179768944591:0.0474089139984578!GTF2F1#2962;23:2.93012200165426:2.37330285080668e-06:8.41076947524259e-05!HDAC2#3066;27:3.62221746388909:2.9923051691157e-09:2.51216526975301e-07!HEY1#23462;81:3.27248994491563:4.69649341867548e-32:2.05228902156087e-29!HMGN3#9324;43:3.51677552104075:1.52424656447081e-14:2.59691332702719e-12!IRF1#3659;53:4.04769678938887:2.04592402286147e-21:5.5212986827811e-19!JUN#3725;18:2.25230925462054:0.000916731689443765:0.00667009481077172!JUNB#3726;10:3.06106326598211:0.00164104557276028:0.0102689729522774!JUND#3727;42:2.93775885558583:1.53791075711911e-11:1.87637688741545e-09!MAX#4149;47:3.03270108923335:1.20648434528408e-13:1.87505979965958e-11!MXI1#4601;29:2.8888557723402:1.0151248100384e-07:5.95610224919103e-06!MYC#4609;60:3.13336912296564:2.71818229607302e-19:6.5260745015993e-17!NANOG#79923;10:2.92447784810127:0.002286718477871:0.0129787832786463!NFE2#4778;7:5.40429824561404:0.000340433585019052:0.00346029617380095!NFKB1#4790;66:3.62212185996793:1.06196970810084e-25:3.47683555938382e-23!NFYA#4800;13:2.39532549097797:0.0029831045873481:0.0158785209723281!NFYB#4801;14:2.3463710554951:0.00247794724166859:0.0139204094439581!NR3C1#2908;17:2.54541396629942:0.000328891992780039:0.00335113666672727!NRF1#4899;23:2.80836427297351:4.82223750032897e-06:0.000149445003648919!PAX5#5079;48:3.20139145496536:6.6613006161925e-15:1.16532592136437e-12!PBX3#5090;22:4.82119279108371:7.16328566996639e-10:6.81353726853934e-08!POLR2A#5430;99:2.12597864479249:7.21563982260622e-32:3.12694691880984e-29!POU2F2#5452;49:4.46200078829384:2.83392343672019e-21:7.58902896942615e-19!RAD21#5885;18:1.86390610118214:0.00706795310137437:0.0294784534944466!RDBP#7936;4:6.145536159601:0.00427178985317455:0.0203216480129223!REST#5978;32:3.08800918916097:3.39120772656025e-09:2.79537761447692e-07!RFX5#5993;35:4.21676878951828:6.7233324272251e-14:1.07531104956656e-11!RXRA#6256;11:2.20820788530466:0.0111597109642217:0.0410072849691206!SIN3A#25942;66:3.56986391969799:2.48771504585144e-25:8.01896517511354e-23!SIRT6#51548;4:6.145536159601:0.00427178985317455:0.0203225737018037!SIX5#147912;17:2.90474161042803:6.82161962458413e-05:0.00108919604337554!SMARCB1#6598;18:3.28548884060833:7.85419882956911e-06:0.000222419921789959!SMARCC2#6601;6:5.64932246561386:0.000726355253804798:0.00579392166440994!SMC3#9126;19:2.85853724053724:2.97096671741633e-05:0.00061564443055604!SP1#6667;58:3.30506119932172:1.4307326931881e-19:3.5158656880911e-17!SP2#6668;10:2.61535304938446:0.00502343250548526:0.0234445556993643!SPI1#6688;35:2.87151322798295:3.13697436304395e-09:2.61679285544686e-07!SREBF1#6720;10:4.70058494404883:5.70720935902288e-05:0.000951860808442973!SRF#6722;20:2.75943565243356:2.92377694852298e-05:0.000609615373780777!STAT1#6772;13:2.6918563746359:0.00106900362805714:0.0075502583289822!STAT3#6774;18:1.89350369948776:0.00602597923153659:0.0270059751528686!TAF1#6872;90:3.00874165717076:3.33115134962077e-36:1.70540252844629e-33!TAF7#6879;35:4.00157429172337:3.10324443152333e-13:4.59715950615411e-11!TBP#6908;82:3.03955196341904:2.45123624291933e-30:9.96127089393978e-28!TCF12#6938;35:3.72206271576525:2.49493361155037e-12:3.37087155830154e-10!TCF7L2#6934;25:2.69254414078434:3.55040604980343e-06:0.000117230748477844!TFAP2A#7020;16:2.64298149968719:0.000332833883788873:0.0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|tf_chipseq_enrich=ATF3#467;22:4.94189839572193:4.52899345798051e-10:4.40823436866753e-08!BHLHE40#8553;10:4.48718135469774:8.36338657560895e-05:0.00125587883618983!BRCA1#672;30:6.05526919296713:6.48206509114599e-16:1.23536568623028e-13!CCNT2#905;61:3.86508296194721:1.48055951119461e-24:4.62958547274412e-22!CEBPB#1051;33:2.63047871652219:9.03368834232657e-08:5.33938526759618e-06!CHD2#1106;37:3.82728844862324:1.91838667119907e-13:2.91212769699651e-11!CTCF#10664;35:1.87608973057626:8.15192580369663e-05:0.00123459828743079!CTCFL#140690;13:2.56704166666667:0.00163419287879483:0.0102273172380425!E2F1#1869;63:3.09165520537397:2.53989391911509e-20:6.54972792638174e-18!E2F4#1874;26:3.29369568197395:4.37523793755356e-08:2.87026052110651e-06!E2F6#1876;53:2.65909253779961:2.29988462341672e-13:3.45608129762617e-11!EBF1#1879;24:2.13755204317656:0.000239502796000365:0.00260692365935197!EGR1#1958;63:3.14255282973039:1.05354879233456e-20:2.76461262117158e-18!ELF1#1997;71:3.02324955075335:1.23175375566203e-23:3.73962588626706e-21!ELK4#2005;20:3.24713633169361:2.68981593024684e-06:9.4142656145794e-05!EP300#2033;32:2.16766135239142:1.08405238420193e-05:0.000281006073352358!ETS1#2113;38:3.69692915043689:2.31101688740571e-13:3.46782029746788e-11!FOS#2353;22:1.97955016795677:0.00129031842800045:0.00864896773647002!FOSL1#8061;7:2.77995058014611:0.0134267295063494:0.0474366294412784!FOSL2#2355;23:3.89394613904919:1.55161625843908e-08:1.13718772221136e-06!FOXA1#3169;28:3.10279752982793:4.06103716942618e-08:2.68097762918901e-06!GABPB1#2553;48:3.39248824136744:6.77337332062742e-16:1.28853248858471e-13!GATA1#2623;18:2.44085546588408:0.00035665791529376:0.00356722811869038!GTF2B#2959;8:2.55550639474594:0.0134179768944591:0.0474089139984578!GTF2F1#2962;23:2.93012200165426:2.37330285080668e-06:8.41076947524259e-05!HDAC2#3066;27:3.62221746388909:2.9923051691157e-09:2.51216526975301e-07!HEY1#23462;81:3.27248994491563:4.69649341867548e-32:2.05228902156087e-29!HMGN3#9324;43:3.51677552104075:1.52424656447081e-14:2.59691332702719e-12!IRF1#3659;53:4.04769678938887:2.04592402286147e-21:5.5212986827811e-19!JUN#3725;18:2.25230925462054:0.000916731689443765:0.00667009481077172!JUNB#3726;10:3.06106326598211:0.00164104557276028:0.0102689729522774!JUND#3727;42:2.93775885558583:1.53791075711911e-11:1.87637688741545e-09!MAX#4149;47:3.03270108923335:1.20648434528408e-13:1.87505979965958e-11!MXI1#4601;29:2.8888557723402:1.0151248100384e-07:5.95610224919103e-06!MYC#4609;60:3.13336912296564:2.71818229607302e-19:6.5260745015993e-17!NANOG#79923;10:2.92447784810127:0.002286718477871:0.0129787832786463!NFE2#4778;7:5.40429824561404:0.000340433585019052:0.00346029617380095!NFKB1#4790;66:3.62212185996793:1.06196970810084e-25:3.47683555938382e-23!NFYA#4800;13:2.39532549097797:0.0029831045873481:0.0158785209723281!NFYB#4801;14:2.3463710554951:0.00247794724166859:0.0139204094439581!NR3C1#2908;17:2.54541396629942:0.000328891992780039:0.00335113666672727!NRF1#4899;23:2.80836427297351:4.82223750032897e-06:0.000149445003648919!PAX5#5079;48:3.20139145496536:6.6613006161925e-15:1.16532592136437e-12!PBX3#5090;22:4.82119279108371:7.16328566996639e-10:6.81353726853934e-08!POLR2A#5430;99:2.12597864479249:7.21563982260622e-32:3.12694691880984e-29!POU2F2#5452;49:4.46200078829384:2.83392343672019e-21:7.58902896942615e-19!RAD21#5885;18:1.86390610118214:0.00706795310137437:0.0294784534944466!RDBP#7936;4:6.145536159601:0.00427178985317455:0.0203216480129223!REST#5978;32:3.08800918916097:3.39120772656025e-09:2.79537761447692e-07!RFX5#5993;35:4.21676878951828:6.7233324272251e-14:1.07531104956656e-11!RXRA#6256;11:2.20820788530466:0.0111597109642217:0.0410072849691206!SIN3A#25942;66:3.56986391969799:2.48771504585144e-25:8.01896517511354e-23!SIRT6#51548;4:6.145536159601:0.00427178985317455:0.0203225737018037!SIX5#147912;17:2.90474161042803:6.82161962458413e-05:0.00108919604337554!SMARCB1#6598;18:3.28548884060833:7.85419882956911e-06:0.000222419921789959!SMARCC2#6601;6:5.64932246561386:0.000726355253804798:0.00579392166440994!SMC3#9126;19:2.85853724053724:2.97096671741633e-05:0.00061564443055604!SP1#6667;58:3.30506119932172:1.4307326931881e-19:3.5158656880911e-17!SP2#6668;10:2.61535304938446:0.00502343250548526:0.0234445556993643!SPI1#6688;35:2.87151322798295:3.13697436304395e-09:2.61679285544686e-07!SREBF1#6720;10:4.70058494404883:5.70720935902288e-05:0.000951860808442973!SRF#6722;20:2.75943565243356:2.92377694852298e-05:0.000609615373780777!STAT1#6772;13:2.6918563746359:0.00106900362805714:0.0075502583289822!STAT3#6774;18:1.89350369948776:0.00602597923153659:0.0270059751528686!TAF1#6872;90:3.00874165717076:3.33115134962077e-36:1.70540252844629e-33!TAF7#6879;35:4.00157429172337:3.10324443152333e-13:4.59715950615411e-11!TBP#6908;82:3.03955196341904:2.45123624291933e-30:9.96127089393978e-28!TCF12#6938;35:3.72206271576525:2.49493361155037e-12:3.37087155830154e-10!TCF7L2#6934;25:2.69254414078434:3.55040604980343e-06:0.000117230748477844!TFAP2A#7020;16:2.64298149968719:0.000332833883788873:0.0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}}
}}

Revision as of 13:41, 26 November 2012


Full id: C175_Eosinophils_Neutrophils_CD4_Basophils_CD19_CD8_Natural



Phase1 CAGE Peaks


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data




Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>



Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467224.941898395721934.52899345798051e-104.40823436866753e-08
BHLHE40#8553104.487181354697748.36338657560895e-050.00125587883618983
BRCA1#672306.055269192967136.48206509114599e-161.23536568623028e-13
CCNT2#905613.865082961947211.48055951119461e-244.62958547274412e-22
CEBPB#1051332.630478716522199.03368834232657e-085.33938526759618e-06
CHD2#1106373.827288448623241.91838667119907e-132.91212769699651e-11
CTCF#10664351.876089730576268.15192580369663e-050.00123459828743079
CTCFL#140690132.567041666666670.001634192878794830.0102273172380425
E2F1#1869633.091655205373972.53989391911509e-206.54972792638174e-18
E2F4#1874263.293695681973954.37523793755356e-082.87026052110651e-06
E2F6#1876532.659092537799612.29988462341672e-133.45608129762617e-11
EBF1#1879242.137552043176560.0002395027960003650.00260692365935197
EGR1#1958633.142552829730391.05354879233456e-202.76461262117158e-18
ELF1#1997713.023249550753351.23175375566203e-233.73962588626706e-21
ELK4#2005203.247136331693612.68981593024684e-069.4142656145794e-05
EP300#2033322.167661352391421.08405238420193e-050.000281006073352358
ETS1#2113383.696929150436892.31101688740571e-133.46782029746788e-11
FOS#2353221.979550167956770.001290318428000450.00864896773647002
FOSL1#806172.779950580146110.01342672950634940.0474366294412784
FOSL2#2355233.893946139049191.55161625843908e-081.13718772221136e-06
FOXA1#3169283.102797529827934.06103716942618e-082.68097762918901e-06
GABPB1#2553483.392488241367446.77337332062742e-161.28853248858471e-13
GATA1#2623182.440855465884080.000356657915293760.00356722811869038
GTF2B#295982.555506394745940.01341797689445910.0474089139984578
GTF2F1#2962232.930122001654262.37330285080668e-068.41076947524259e-05
HDAC2#3066273.622217463889092.9923051691157e-092.51216526975301e-07
HEY1#23462813.272489944915634.69649341867548e-322.05228902156087e-29
HMGN3#9324433.516775521040751.52424656447081e-142.59691332702719e-12
IRF1#3659534.047696789388872.04592402286147e-215.5212986827811e-19
JUN#3725182.252309254620540.0009167316894437650.00667009481077172
JUNB#3726103.061063265982110.001641045572760280.0102689729522774
JUND#3727422.937758855585831.53791075711911e-111.87637688741545e-09
MAX#4149473.032701089233351.20648434528408e-131.87505979965958e-11
MXI1#4601292.88885577234021.0151248100384e-075.95610224919103e-06
MYC#4609603.133369122965642.71818229607302e-196.5260745015993e-17
NANOG#79923102.924477848101270.0022867184778710.0129787832786463
NFE2#477875.404298245614040.0003404335850190520.00346029617380095
NFKB1#4790663.622121859967931.06196970810084e-253.47683555938382e-23
NFYA#4800132.395325490977970.00298310458734810.0158785209723281
NFYB#4801142.34637105549510.002477947241668590.0139204094439581
NR3C1#2908172.545413966299420.0003288919927800390.00335113666672727
NRF1#4899232.808364272973514.82223750032897e-060.000149445003648919
PAX5#5079483.201391454965366.6613006161925e-151.16532592136437e-12
PBX3#5090224.821192791083717.16328566996639e-106.81353726853934e-08
POLR2A#5430992.125978644792497.21563982260622e-323.12694691880984e-29
POU2F2#5452494.462000788293842.83392343672019e-217.58902896942615e-19
RAD21#5885181.863906101182140.007067953101374370.0294784534944466
RDBP#793646.1455361596010.004271789853174550.0203216480129223
REST#5978323.088009189160973.39120772656025e-092.79537761447692e-07
RFX5#5993354.216768789518286.7233324272251e-141.07531104956656e-11
RXRA#6256112.208207885304660.01115971096422170.0410072849691206
SIN3A#25942663.569863919697992.48771504585144e-258.01896517511354e-23
SIRT6#5154846.1455361596010.004271789853174550.0203225737018037
SIX5#147912172.904741610428036.82161962458413e-050.00108919604337554
SMARCB1#6598183.285488840608337.85419882956911e-060.000222419921789959
SMARCC2#660165.649322465613860.0007263552538047980.00579392166440994
SMC3#9126192.858537240537242.97096671741633e-050.00061564443055604
SP1#6667583.305061199321721.4307326931881e-193.5158656880911e-17
SP2#6668102.615353049384460.005023432505485260.0234445556993643
SPI1#6688352.871513227982953.13697436304395e-092.61679285544686e-07
SREBF1#6720104.700584944048835.70720935902288e-050.000951860808442973
SRF#6722202.759435652433562.92377694852298e-050.000609615373780777
STAT1#6772132.69185637463590.001069003628057140.0075502583289822
STAT3#6774181.893503699487760.006025979231536590.0270059751528686
TAF1#6872903.008741657170763.33115134962077e-361.70540252844629e-33
TAF7#6879354.001574291723373.10324443152333e-134.59715950615411e-11
TBP#6908823.039551963419042.45123624291933e-309.96127089393978e-28
TCF12#6938353.722062715765252.49493361155037e-123.37087155830154e-10
TCF7L2#6934252.692544140784343.55040604980343e-060.000117230748477844
TFAP2A#7020162.642981499687190.0003328338837888730.00338964778049987
TFAP2C#7022293.134676296859471.71048707958504e-081.23712991762314e-06
TRIM28#10155142.602673506336750.0009404087662723470.00680727412952021
USF1#7391472.989904660287742.05668686044203e-133.10851402341107e-11
USF2#7392334.287425137072972.84639348952087e-134.25285392921416e-11
WRNIP1#5689755.49099821746880.00229471847031290.0130185291064702
YY1#7528582.848479034915241.93123855460159e-163.82001180689462e-14
ZBTB33#1000992.84982525269830.004476332892378150.0211798908597418
ZBTB7A#51341443.234840095465391.26133157086823e-131.95448379717963e-11
ZEB1#6935162.702149122807020.0002602440621345410.00279022991533408
ZNF143#7702182.430157779401020.0003759403196881740.00373469333662258
ZNF263#10127342.795426156583631.15331605152804e-088.64688981374997e-07



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data