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Coexpression cluster:C1453: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0009966!regulation of signal transduction!0.0232625119888189!2786;5909$GO:0008277!regulation of G-protein coupled receptor protein signaling pathway!0.0304795437772065!2786$GO:0005834!heterotrimeric G-protein complex!0.0304795437772065!2786$GO:0019897!extrinsic to plasma membrane!0.0308855156143789!2786
|gostat_on_coexpression_clusters=GO:0009966!regulation of signal transduction!0.0232625119888189!2786;5909$GO:0008277!regulation of G-protein coupled receptor protein signaling pathway!0.0304795437772065!2786$GO:0005834!heterotrimeric G-protein complex!0.0304795437772065!2786$GO:0019897!extrinsic to plasma membrane!0.0308855156143789!2786
|id=C1453
|id=C1453
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000181!3.42e-20!12;CL:0000417!3.42e-20!12;CL:0000668!3.42e-20!12;CL:0000412!3.42e-20!12;CL:0000182!3.42e-20!12;CL:0000167!1.10e-10!1;CL:0000164!1.10e-10!1;CL:0000502!1.10e-10!1;CL:0000172!1.10e-10!1;CL:0000173!1.10e-10!1;CL:0002351!1.10e-10!1;CL:0002563!1.69e-10!4;CL:0000223!1.11e-09!58
|ontology_enrichment_disease=DOID:3119!2.90e-07!14
|ontology_enrichment_disease=DOID:4430!1.10e-10!1;DOID:7!1.77e-08!39
|ontology_enrichment_uberon=UBERON:0007023!4.92e-15!115;UBERON:0001049!5.45e-12!57;UBERON:0005068!5.45e-12!57;UBERON:0006241!5.45e-12!57;UBERON:0007135!5.45e-12!57;UBERON:0005743!1.06e-11!86;UBERON:0001017!1.11e-11!82;UBERON:0000073!1.12e-10!94;UBERON:0001016!1.12e-10!94;UBERON:0002616!2.47e-10!59;UBERON:0003080!6.84e-09!42;UBERON:0003075!1.20e-08!86;UBERON:0007284!1.20e-08!86;UBERON:0000955!1.63e-08!69;UBERON:0006238!1.63e-08!69;UBERON:0002780!5.11e-08!41;UBERON:0001890!5.11e-08!41;UBERON:0006240!5.11e-08!41;UBERON:0002346!6.02e-08!90;UBERON:0001869!3.44e-07!32;UBERON:0001950!5.39e-07!20;UBERON:0002020!8.98e-07!34;UBERON:0003528!8.98e-07!34
|ontology_enrichment_uberon=UBERON:0002107!4.91e-18!19;UBERON:0006925!4.91e-18!19;UBERON:0008836!4.91e-18!19;UBERON:0008835!1.60e-15!22;UBERON:0003894!1.60e-15!22;UBERON:0009854!7.88e-15!23;UBERON:0002365!1.50e-14!31;UBERON:0002330!1.50e-14!31;UBERON:0007499!1.31e-13!25;UBERON:0009497!1.31e-13!25;UBERON:0000015!1.31e-13!25;UBERON:0002423!1.31e-13!25;UBERON:0006235!1.31e-13!25;UBERON:0004161!1.31e-13!25;UBERON:0003929!2.91e-13!54;UBERON:0009856!4.52e-13!26;UBERON:0002368!6.90e-13!35;UBERON:0002530!5.50e-12!59;UBERON:0001242!1.69e-10!4;UBERON:0001262!1.69e-10!4;UBERON:0004786!1.69e-10!4;UBERON:0004808!1.69e-10!4;UBERON:0001277!1.69e-10!4;UBERON:0002581!1.77e-10!1;UBERON:0000949!7.31e-10!45;UBERON:0005911!2.62e-08!82;UBERON:0005172!4.34e-08!54;UBERON:0005173!4.34e-08!54;UBERON:0002417!3.32e-07!60;UBERON:0000916!3.32e-07!60
|tf_chipseq_enrich=EP300#2033;6:6.7739417262232:1.03454107484288e-05:0.000269644210919679!FOSL2#2355;4:11.2868004030411:0.000165665772215763:0.00203792315482239!FOXA1#3169;5:9.23451645782121:3.31890114386024e-05:0.000659982323997753!FOXA2#3170;5:20.5253864605544:6.3869668268396e-07:2.91160379060803e-05!HDAC2#3066;5:11.1796835305219:1.29408913564529e-05:0.000316963825604264!HEY1#23462;5:3.36675920258809:0.00442382704520303:0.020951390929347!HNF4A#3172;5:19.2769086357947:8.72194926701819e-07:3.78600024729058e-05!HNF4G#3174;5:23.9611854387057:2.95997618535695e-07:1.49630664483298e-05!RXRA#6256;4:13.3830780927555:8.51052088844461e-05:0.0012765047983172!SIN3A#25942;4:3.60592315121009:0.0127389384448714:0.0459422629318664!SP1#6667;6:5.6983813781409:2.91961319085282e-05:0.000609842964078956!TCF7L2#6934;4:7.18011770875823:0.000955329712067973:0.00687620122664831!TRIM28#10155;3:9.29526252263126:0.0027513650505949:0.0150926947066065!USF1#7391;4:4.24099951813864:0.00700536775082942:0.0296064099437064
|tf_chipseq_enrich=EP300#2033;6:6.7739417262232:1.03454107484288e-05:0.000269644210919679!FOSL2#2355;4:11.2868004030411:0.000165665772215763:0.00203792315482239!FOXA1#3169;5:9.23451645782121:3.31890114386024e-05:0.000659982323997753!FOXA2#3170;5:20.5253864605544:6.3869668268396e-07:2.91160379060803e-05!HDAC2#3066;5:11.1796835305219:1.29408913564529e-05:0.000316963825604264!HEY1#23462;5:3.36675920258809:0.00442382704520303:0.020951390929347!HNF4A#3172;5:19.2769086357947:8.72194926701819e-07:3.78600024729058e-05!HNF4G#3174;5:23.9611854387057:2.95997618535695e-07:1.49630664483298e-05!RXRA#6256;4:13.3830780927555:8.51052088844461e-05:0.0012765047983172!SIN3A#25942;4:3.60592315121009:0.0127389384448714:0.0459422629318664!SP1#6667;6:5.6983813781409:2.91961319085282e-05:0.000609842964078956!TCF7L2#6934;4:7.18011770875823:0.000955329712067973:0.00687620122664831!TRIM28#10155;3:9.29526252263126:0.0027513650505949:0.0150926947066065!USF1#7391;4:4.24099951813864:0.00700536775082942:0.0296064099437064
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}}
}}

Revision as of 11:18, 19 October 2012


Full id: C1453_argyrophil_hepatocellular_Intestinal_small_liver_hepatoblastoma_gastrointestinal



Phase1 CAGE Peaks

Hg19::chr19:36611472..36611485,+p@chr19:36611472..36611485
+
Hg19::chr1:117008831..117008843,+p@chr1:117008831..117008843
+
Hg19::chr1:117008851..117008867,+p@chr1:117008851..117008867
+
Hg19::chr1:21996297..21996310,-p9@RAP1GAP
Hg19::chr1:235814345..235814362,-p9@GNG4
Hg19::chr9:139693833..139693853,+p10@KIAA1984


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


GO IDGO nameFDR corrected p-value
GO:0009966regulation of signal transduction0.0232625119888189
GO:0008277regulation of G-protein coupled receptor protein signaling pathway0.0304795437772065
GO:0005834heterotrimeric G-protein complex0.0304795437772065
GO:0019897extrinsic to plasma membrane0.0308855156143789



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
liver4.91e-1819
digestive gland4.91e-1819
liver bud4.91e-1819
hepatic diverticulum1.60e-1522
liver primordium1.60e-1522
digestive tract diverticulum7.88e-1523
exocrine gland1.50e-1431
exocrine system1.50e-1431
epithelial sac1.31e-1325
epithelium of foregut-midgut junction1.31e-1325
anatomical boundary1.31e-1325
hepatobiliary system1.31e-1325
foregut-midgut junction1.31e-1325
septum transversum1.31e-1325
gut epithelium2.91e-1354
sac4.52e-1326
endocrine gland6.90e-1335
gland5.50e-1259
intestinal mucosa1.69e-104
wall of intestine1.69e-104
gastrointestinal system mucosa1.69e-104
gastrointestinal system epithelium1.69e-104
intestinal epithelium1.69e-104
postcentral gyrus1.77e-101
endocrine system7.31e-1045
endo-epithelium2.62e-0882
abdomen element4.34e-0854
abdominal segment element4.34e-0854
abdominal segment of trunk3.32e-0760
abdomen3.32e-0760
Disease
Ontology termp-valuen
somatostatinoma1.10e-101
disease of anatomical entity1.77e-0839


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
EP300#203366.77394172622321.03454107484288e-050.000269644210919679
FOSL2#2355411.28680040304110.0001656657722157630.00203792315482239
FOXA1#316959.234516457821213.31890114386024e-050.000659982323997753
FOXA2#3170520.52538646055446.3869668268396e-072.91160379060803e-05
HDAC2#3066511.17968353052191.29408913564529e-050.000316963825604264
HEY1#2346253.366759202588090.004423827045203030.020951390929347
HNF4A#3172519.27690863579478.72194926701819e-073.78600024729058e-05
HNF4G#3174523.96118543870572.95997618535695e-071.49630664483298e-05
RXRA#6256413.38307809275558.51052088844461e-050.0012765047983172
SIN3A#2594243.605923151210090.01273893844487140.0459422629318664
SP1#666765.69838137814092.91961319085282e-050.000609842964078956
TCF7L2#693447.180117708758230.0009553297120679730.00687620122664831
TRIM28#1015539.295262522631260.00275136505059490.0150926947066065
USF1#739144.240999518138640.007005367750829420.0296064099437064



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.