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Coexpression cluster:C1088: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;8:22.4631745260087:1.53751153688198e-11:1.87808382924464e-09!BHLHE40#8553;8:44.8718135469774:6.04397679531981e-14:9.72614626388914e-12!BRCA1#672;8:20.1842306432238:3.61942729088439e-11:4.1448395486039e-09!CEBPB#1051;8:7.97114762582482:6.12878626083745e-08:3.7987199305377e-06!ELF1#1997;8:4.25809795880754:9.24826870984006e-06:0.000246523720211074!EP300#2033;8:6.7739417262232:2.25366016107097e-07:1.19174690411185e-05!FOS#2353;8:8.9979553088944:2.32446530602145e-08:1.63808928539524e-06!FOSL2#2355;8:16.9302006045617:1.47793326491323e-10:1.56545509385672e-08!FOXA1#3169;8:11.0814197493855:4.39110036332964e-09:3.56057555004491e-07!FOXA2#3170;8:24.6304637526652:7.35637804493982e-12:9.33527055450146e-10!GTF2F1#2962;8:12.7396608767577:1.43868108630934e-09:1.2831290689416e-07!HDAC2#3066;8:13.4156202366263:9.51254966654288e-10:8.87036763057207e-08!HEY1#23462;8:4.04011104310571:1.4081650274634e-05:0.000339255703121685!HNF4A#3172;8:23.1322903629537:1.21561011047446e-11:1.50959695990299e-09!JUN#3725;8:12.5128291923363:1.66110954195842e-09:1.45662988625185e-07!JUND#3727;8:6.99466394187103:1.74369580801501e-07:9.57968682237137e-06!MAX#4149;8:6.45255550900712:3.32496617557502e-07:1.65992419890478e-05!NR3C1#2908;8:14.973023331173:3.9500670680339e-10:3.89557180848341e-08!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127251978987234!RAD21#5885;8:10.3550338954563:7.55391711153941e-09:5.84821014982998e-07!RXRA#6256;8:20.0746171391333:3.7806502647693e-11:4.31999270243152e-09!SMARCC1#6599;8:43.6633593196315:7.52062965894322e-14:1.19187714863486e-11!SMC3#9126;8:15.0449328449328:3.80148882898722e-10:3.77398946588019e-08!SP1#6667;8:5.6983813781409:8.98832477855329e-07:3.86627533586214e-05!SPI1#6688;6:6.15324263139204:7.3612205654473e-05:0.00114866056272934!STAT1#6772;8:20.7065874971992:2.95008695392417e-11:3.42718722336915e-09!STAT3#6774;8:10.5194649971542:6.65923543127245e-09:5.22527339749559e-07!TBP#6908;8:3.70677068709639:2.80450451364125e-05:0.000592434560882237!TCF7L2#6934;8:10.7701765631373:5.51536816569572e-09:4.40381908147626e-07!TRIM28#10155;8:18.5905250452625:6.99051420669847e-11:7.70129022398082e-09!USF1#7391;8:6.36149927720796:3.72538670743375e-07:1.83353281026236e-05
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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0151272,0.341646,3.10898,0.301904,0.480078,0.554663,1.68265,0.555925,0.0394821,0.450635,0.597407,0.152895,0.543352,0.300614,0.322799,0.774423,0.250594,0.163559,0.264925,0.341703,0.047825,0.472508,2.23515,0.385586,0.619829,0.135503,0.470396,0.304828,0.122648,0.429397,0.810962,2.58859,0.469827,0.269459,0.0137136,0.266487,0.481208,0.244807,0.174436,0.739305,0.413601,0.0547276,0.299183,0.0169887,0.371118,0.555735,0.440085,0.0498256,0.304949,0.63387,0.567337,0.0927889,0.887323,1.03948,0.546236,0.308962,0.514077,0.776738,0.513089,0.85167,0.558065,1.06063,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,5.92264,0.0911419,1.03748,0.149081,0.138565,0.127753,0.730167,0.797419,0.379656,0.50159,0.745864,0.575394,1.07768,0.986227,0.0220225,0.0757344,0.118789,0.659621,1.59442,1.22073,0.959334,6.10316,0.227232,0.302606,0.239285,0.162291,0.87,0.664183,0.106284,0.246049,0.822041,0.864454,1.83155,0.701386,0.446229,0.762347,2.29252,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,5.75403,0.0278613,0.428232,0.710479,3.49131,10.7963,0.657218,0.477387,1.43278,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,4.45948,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,3.33101,0.703126,0.505785,5.35007,1.88987,1.86008,0.224241,0.0833399,0.0510299,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,3.56519,10.7478,0.36101,0.71907,0.574616,0.213234,2.33631,0.00340764
}}
}}

Revision as of 14:40, 26 November 2012


Full id: C1088_liver_giant_anaplastic_glassy_bile_Hepatocyte_prostate



Phase1 CAGE Peaks

Hg19::chr6:64237703..64237708,+p@chr6:64237703..64237708
+
Hg19::chr6:64237756..64237769,+p@chr6:64237756..64237769
+
Hg19::chr6:64237780..64237794,+p@chr6:64237780..64237794
+
Hg19::chr6:64237801..64237820,+p@chr6:64237801..64237820
+
Hg19::chr6:64237829..64237843,+p@chr6:64237829..64237843
+
Hg19::chr6:64237863..64237874,+p@chr6:64237863..64237874
+
Hg19::chr6:64237875..64237910,+p@chr6:64237875..64237910
+
Hg19::chr6:64237919..64237932,+p@chr6:64237919..64237932
+


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

No GOStat results

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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
larynx3.70e-189
endoderm-derived structure1.06e-15160
endoderm1.06e-15160
presumptive endoderm1.06e-15160
respiratory system2.16e-1374
exocrine gland2.74e-1231
exocrine system2.74e-1231
digestive system1.26e-11145
digestive tract1.26e-11145
primitive gut1.26e-11145
epithelium of foregut-midgut junction3.94e-1125
anatomical boundary3.94e-1125
hepatobiliary system3.94e-1125
foregut-midgut junction3.94e-1125
septum transversum3.94e-1125
gland6.56e-1159
hepatic diverticulum7.17e-1122
liver primordium7.17e-1122
gut epithelium1.06e-1054
foregut1.31e-1087
respiratory tract1.71e-1054
liver2.52e-1019
digestive gland2.52e-1019
liver bud2.52e-1019
digestive tract diverticulum2.64e-1023
upper respiratory tract8.13e-1019
endo-epithelium1.58e-0982
epithelial sac2.61e-0925
subdivision of digestive tract6.90e-09118
sac7.18e-0926
gingival epithelium9.69e-093
acellular anatomical structure1.08e-083
egg chorion1.08e-083
respiratory primordium1.20e-0738
endoderm of foregut1.20e-0738
endocrine gland2.70e-0735
skin gland6.47e-072
epidermis gland6.47e-072
gland of integumental system6.47e-072
sebaceous gland6.47e-072
skin sebaceous gland6.47e-072
sweat gland6.47e-072
sweat gland placode6.47e-072
sebaceous gland placode6.47e-072
mouth mucosa9.15e-0713
segment of respiratory tract9.57e-0747
Disease
Ontology termp-valuen
carcinoma1.25e-12106
cell type cancer3.65e-09143


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

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



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#467822.46317452600871.53751153688198e-111.87808382924464e-09
BHLHE40#8553844.87181354697746.04397679531981e-149.72614626388914e-12
BRCA1#672820.18423064322383.61942729088439e-114.1448395486039e-09
CEBPB#105187.971147625824826.12878626083745e-083.7987199305377e-06
ELF1#199784.258097958807549.24826870984006e-060.000246523720211074
EP300#203386.77394172622322.25366016107097e-071.19174690411185e-05
FOS#235388.99795530889442.32446530602145e-081.63808928539524e-06
FOSL2#2355816.93020060456171.47793326491323e-101.56545509385672e-08
FOXA1#3169811.08141974938554.39110036332964e-093.56057555004491e-07
FOXA2#3170824.63046375266527.35637804493982e-129.33527055450146e-10
GTF2F1#2962812.73966087675771.43868108630934e-091.2831290689416e-07
HDAC2#3066813.41562023662639.51254966654288e-108.87036763057207e-08
HEY1#2346284.040111043105711.4081650274634e-050.000339255703121685
HNF4A#3172823.13229036295371.21561011047446e-111.50959695990299e-09
JUN#3725812.51282919233631.66110954195842e-091.45662988625185e-07
JUND#372786.994663941871031.74369580801501e-079.57968682237137e-06
MAX#414986.452555509007123.32496617557502e-071.65992419890478e-05
NR3C1#2908814.9730233311733.9500670680339e-103.89557180848341e-08
POLR2A#543082.147453176558070.002210725788971910.0127251978987234
RAD21#5885810.35503389545637.55391711153941e-095.84821014982998e-07
RXRA#6256820.07461713913333.7806502647693e-114.31999270243152e-09
SMARCC1#6599843.66335931963157.52062965894322e-141.19187714863486e-11
SMC3#9126815.04493284493283.80148882898722e-103.77398946588019e-08
SP1#666785.69838137814098.98832477855329e-073.86627533586214e-05
SPI1#668866.153242631392047.3612205654473e-050.00114866056272934
STAT1#6772820.70658749719922.95008695392417e-113.42718722336915e-09
STAT3#6774810.51946499715426.65923543127245e-095.22527339749559e-07
TBP#690883.706770687096392.80450451364125e-050.000592434560882237
TCF7L2#6934810.77017656313735.51536816569572e-094.40381908147626e-07
TRIM28#10155818.59052504526256.99051420669847e-117.70129022398082e-09
USF1#739186.361499277207963.72538670743375e-071.83353281026236e-05



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.

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