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Coexpression cluster:C562: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;4:5.61579363150219:0.00464141212767522:0.0219123244373145!BRCA1#672;4:5.04605766080594:0.00677897669640447:0.0287730450782649!CCNT2#905;12:4.75215118272197:2.31381839264867e-07:1.21985299904005e-05!CHD2#1106;6:3.87900856279382:0.00277317152827015:0.0151923657805815!CTCFL#140690;6:7.40492788461538:8.67296992239919e-05:0.0012991914884186!E2F1#1869;9:2.76040643336962:0.00169642820214106:0.0105996568952085!E2F4#1874;5:3.95876884852639:0.00638275993940918:0.0277846392677541!E2F6#1876;13:4.07643903200413:2.37289564027328e-07:1.2459670576898e-05!EBF1#1879;7:3.89657924537394:0.00102115841479567:0.00724368428192929!ELF1#1997;15:3.99196683638207:4.54061180224701e-09:3.66757119887761e-07!ELK4#2005;11:11.1620311401968:1.57457980886855e-10:1.65941009746137e-08!ESR1#2099;3:5.76911311802897:0.0139904224229487:0.0491157930495255!ETS1#2113;15:9.12071336456469:2.17334805334434e-14:3.66100479585854e-12!GABPB1#2553;12:5.30076287713663:6.68540345520611e-08:4.06886277073585e-06!HEY1#23462;16:4.04011104310571:1.98084199021544e-10:2.05031869788018e-08!HMGN3#9324;8:4.0892738616753:0.000257285293595512:0.00276816923640896!IRF1#3659;11:5.25055008057518:4.46896063357945e-07:2.12731895902645e-05!JUND#3727;11:4.80883146003633:1.10371712893257e-06:4.57788376602813e-05!MAX#4149;9:3.62956247381651:0.000207178817062783:0.00243501558352689!MXI1#4601;9:5.6033840411771:6.10807177715345e-06:0.000181640349753454!MYC#4609;13:4.24310402068264:1.44725283711898e-07:8.17909302250373e-06!NFKB1#4790;8:2.74403171209692:0.00385616313935589:0.0190246975346587!NFYA#4800;4:4.60639517495763:0.00932026722368585:0.0352055911090646!NFYB#4801;7:7.3324095484222:1.90141463325496e-05:0.000430669795884872!NRF1#4899;8:6.10513972385545:1.42402144556288e-05:0.00034063988949414!PAX5#5079;12:5.00217414838337:1.2934425150475e-07:7.37770851059781e-06!POLR2A#5430;16:2.14745317655807:4.88536678567824e-06:0.000151042872033585!POU2F2#5452;10:5.69132753608908:1.08661015877248e-06:4.51589647322081e-05!REST#5978;7:4.22188756330601:0.000627281365604383:0.0051633542356838!RXRA#6256;4:5.01865428478332:0.00690995175201785:0.0292576198422522!SIN3A#25942;15:5.07082943138919:1.3297899225369e-10:1.42297059139172e-08!SIX5#147912;9:9.61127738744569:6.29588488815385e-08:3.88614611012943e-06!SP1#6667;13:4.62993486973948:4.9106978951726e-08:3.16195053929674e-06!SPI1#6688;9:4.61493197354403:3.01826774164688e-05:0.000620643561074736!SRF#6722;8:6.8985891310839:5.75315050227476e-06:0.000172857677015844!TAF1#6872;15:3.13410589288621:1.57946317760101e-07:8.84016906781733e-06!TAF7#6879;7:5.00196786465421:0.000219506557872768:0.00248752662735178!TBP#6908;15:3.47509751915286:3.48271765686805e-08:2.32564929261919e-06!TCF12#6938;6:3.98792433831991:0.00240605767871516:0.0135669073484144!TCF7L2#6934;6:4.0388162111765:0.00225404522645573:0.0128037762104759!THAP1#55145;6:11.7634292260692:6.36151165140569e-06:0.000187627764857712!YY1#7528;13:3.99032623425626:3.08644499595592e-07:1.54973667756077e-05!ZNF263#10127;6:3.083190613879:0.00873468672710712:0.0331832944269885
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|tfbs_overrepresentation_for_novel_motifs=0.47731,1.36836,0.464859,0.258928,0.125522,0.25764,0.318839,0.470337,0.463955,1.55472,0.660906,0.355038,0.156166,0.832947,0.124662,0.139688,0.511522,0.0927064,0.689727,0.306606,0.152859,0.765208,2.8001,0.12232,0.542899,0.374311,0.131361,0.249905,2.54189,0.509928,0.622094,0.544857,0.260283,1.01329,0.694555,0.266293,2.9378,1.32193,0.299553,0.188103,0.103604,0.593399,0.097714,0.123709,2.51637,0.517036,0.319738,0.226038,0.0287054,0.400978,0.386472,2.39539,0.377869,0.615394,0.758742,0.311792,0.130259,0.2852,0.509529,2.17125,0.582323,0.321692,0.465207,0.48664,1.60425,0.456015,0.843028,1.20113,0.535417,1.04233,0.19602,0.0621482,6.3164,0.756844,1.39608,1.76898,0.288432,0.471562,0.532468,0.532279,0.177931,0.48568,0.336303,0.0607686,0.70821,4.74118,0.149619,0.263815,1.05319,1.29895,0.932961,0.68283,0.560183,0.0788172,11.6496,0.0858933,0.0444202,1.45968,0.412954,0.437614,0.0899484,0.555021,0.594155,0.514828,0.445845,3.49969,1.25067,0.826592,4.80602,3.86226,0.938911,1.44351,0.455599,0.677747,0.886618,0.333119,1.24584,0.216858,0.453946,0.0803321,0.748992,0.406842,0.255485,0.345739,0.993708,0.472239,0.313614,1.38691,0.78949,0.0864157,0.683478,0.219902,0.803201,0.342946,0.945426,0.469273,0.21329,0.250344,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,0.76278,0.432737,1.59165,0.203207,0.953427,0.850402,10.1794,0.683836,0.201134,0.859679,1.07219,0.394947,0.116843,0.184652,1.52332,0.867287,0.66649,0.531753,0.166635,0.46162,0.335644,0.530837,0.317742,4.11341
}}
}}

Revision as of 14:18, 26 November 2012


Full id: C562_Smooth_Fibroblast_Preadipocyte_Hepatic_Alveolar_Adipocyte_Mesenchymal



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


No results for this coexpression

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#46745.615793631502190.004641412127675220.0219123244373145
BRCA1#67245.046057660805940.006778976696404470.0287730450782649
CCNT2#905124.752151182721972.31381839264867e-071.21985299904005e-05
CHD2#110663.879008562793820.002773171528270150.0151923657805815
CTCFL#14069067.404927884615388.67296992239919e-050.0012991914884186
E2F1#186992.760406433369620.001696428202141060.0105996568952085
E2F4#187453.958768848526390.006382759939409180.0277846392677541
E2F6#1876134.076439032004132.37289564027328e-071.2459670576898e-05
EBF1#187973.896579245373940.001021158414795670.00724368428192929
ELF1#1997153.991966836382074.54061180224701e-093.66757119887761e-07
ELK4#20051111.16203114019681.57457980886855e-101.65941009746137e-08
ESR1#209935.769113118028970.01399042242294870.0491157930495255
ETS1#2113159.120713364564692.17334805334434e-143.66100479585854e-12
GABPB1#2553125.300762877136636.68540345520611e-084.06886277073585e-06
HEY1#23462164.040111043105711.98084199021544e-102.05031869788018e-08
HMGN3#932484.08927386167530.0002572852935955120.00276816923640896
IRF1#3659115.250550080575184.46896063357945e-072.12731895902645e-05
JUND#3727114.808831460036331.10371712893257e-064.57788376602813e-05
MAX#414993.629562473816510.0002071788170627830.00243501558352689
MXI1#460195.60338404117716.10807177715345e-060.000181640349753454
MYC#4609134.243104020682641.44725283711898e-078.17909302250373e-06
NFKB1#479082.744031712096920.003856163139355890.0190246975346587
NFYA#480044.606395174957630.009320267223685850.0352055911090646
NFYB#480177.33240954842221.90141463325496e-050.000430669795884872
NRF1#489986.105139723855451.42402144556288e-050.00034063988949414
PAX5#5079125.002174148383371.2934425150475e-077.37770851059781e-06
POLR2A#5430162.147453176558074.88536678567824e-060.000151042872033585
POU2F2#5452105.691327536089081.08661015877248e-064.51589647322081e-05
REST#597874.221887563306010.0006272813656043830.0051633542356838
RXRA#625645.018654284783320.006909951752017850.0292576198422522
SIN3A#25942155.070829431389191.3297899225369e-101.42297059139172e-08
SIX5#14791299.611277387445696.29588488815385e-083.88614611012943e-06
SP1#6667134.629934869739484.9106978951726e-083.16195053929674e-06
SPI1#668894.614931973544033.01826774164688e-050.000620643561074736
SRF#672286.89858913108395.75315050227476e-060.000172857677015844
TAF1#6872153.134105892886211.57946317760101e-078.84016906781733e-06
TAF7#687975.001967864654210.0002195065578727680.00248752662735178
TBP#6908153.475097519152863.48271765686805e-082.32564929261919e-06
TCF12#693863.987924338319910.002406057678715160.0135669073484144
TCF7L2#693464.03881621117650.002254045226455730.0128037762104759
THAP1#55145611.76342922606926.36151165140569e-060.000187627764857712
YY1#7528133.990326234256263.08644499595592e-071.54973667756077e-05
ZNF263#1012763.0831906138790.008734686727107120.0331832944269885



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


This analysis result is provided for C0 - C305 clusters.