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Coexpression cluster:C1223: Difference between revisions

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|tf_chipseq_enrich=ELF1#1997;7:4.25809795880754:3.93848941900192e-05:0.000735309074778588!EP300#2033;7:6.7739417262232:1.52695018318475e-06:5.86513976394382e-05!FOS#2353;7:8.9979553088944:2.09217725654467e-07:1.11881669480936e-05!FOSL2#2355;7:16.9302006045617:2.50368126508949e-09:2.11897866810925e-07!FOXA1#3169;7:11.0814197493855:4.86782131208363e-08:3.14598013621722e-06!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.02234412162372!SIN3A#25942;7:5.40888472681514:7.3795239773719e-06:0.000211617272013384!SP1#6667;7:5.6983813781409:5.12280185510121e-06:0.000157266402982044
|tf_chipseq_enrich=ELF1#1997;7:4.25809795880754:3.93848941900192e-05:0.000735309074778588!EP300#2033;7:6.7739417262232:1.52695018318475e-06:5.86513976394382e-05!FOS#2353;7:8.9979553088944:2.09217725654467e-07:1.11881669480936e-05!FOSL2#2355;7:16.9302006045617:2.50368126508949e-09:2.11897866810925e-07!FOXA1#3169;7:11.0814197493855:4.86782131208363e-08:3.14598013621722e-06!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.02234412162372!SIN3A#25942;7:5.40888472681514:7.3795239773719e-06:0.000211617272013384!SP1#6667;7:5.6983813781409:5.12280185510121e-06:0.000157266402982044
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}}
}}

Revision as of 14:45, 26 November 2012


Full id: C1223_Retinal_tubular_Endothelial_placenta_small_temporal_duodenum



Phase1 CAGE Peaks

Hg19::chr16:82068830..82068841,+p6@HSD17B2
Hg19::chr16:82068851..82068864,+p4@HSD17B2
Hg19::chr16:82068873..82068889,+p3@HSD17B2
Hg19::chr16:82068905..82068918,+p7@HSD17B2
Hg19::chr16:82068920..82068953,+p2@HSD17B2
Hg19::chr16:82068960..82068995,+p1@HSD17B2
Hg19::chr16:82068997..82069008,+p5@HSD17B2


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><br>

Cell Type
Ontology termp-valuen
epithelial cell1.41e-16253
endodermal cell1.72e-1358
embryonic cell3.60e-12250
endo-epithelial cell1.03e-0842
lymphangioblast1.80e-086
endothelial cell of lymphatic vessel1.80e-086
vascular lymphangioblast1.80e-086
metabolising cell2.26e-0712
endopolyploid cell2.26e-0712
parenchymal cell2.26e-0712
polyploid cell2.26e-0712
hepatocyte2.26e-0712
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.06e-19160
endoderm2.06e-19160
presumptive endoderm2.06e-19160
digestive system1.03e-18145
digestive tract1.03e-18145
primitive gut1.03e-18145
subdivision of digestive tract3.07e-18118
gut epithelium9.02e-1754
anatomical cluster1.37e-14373
intestine8.93e-1317
endo-epithelium1.69e-1182
pigment epithelium of eye2.46e-1111
exocrine gland4.52e-1131
exocrine system4.52e-1131
gland5.26e-1159
orifice6.16e-1136
epithelium of foregut-midgut junction1.22e-1025
anatomical boundary1.22e-1025
hepatobiliary system1.22e-1025
foregut-midgut junction1.22e-1025
septum transversum1.22e-1025
digestive tract diverticulum1.65e-1023
hindgut2.03e-1019
multi-tissue structure2.56e-10342
organism subdivision3.87e-10264
hepatic diverticulum6.94e-1022
liver primordium6.94e-1022
head1.15e-0956
gastrointestinal system2.23e-0925
subdivision of head2.37e-0949
eye2.62e-0921
visual system2.62e-0921
organ system subdivision2.75e-09223
cloaca9.17e-0914
anal region9.17e-0914
embryonic cloaca9.17e-0914
terminal part of digestive tract9.17e-0914
primitive urogenital sinus9.17e-0914
proctodeum9.17e-0914
sac1.06e-0826
sense organ1.20e-0824
sensory system1.20e-0824
entire sense organ system1.20e-0824
camera-type eye1.66e-0820
simple eye1.66e-0820
immature eye1.66e-0820
ocular region1.66e-0820
eyeball of camera-type eye1.66e-0820
optic cup1.66e-0820
optic vesicle1.66e-0820
eye primordium1.66e-0820
face1.73e-0822
liver3.15e-0819
digestive gland3.15e-0819
liver bud3.15e-0819
epithelial sac4.02e-0825
genitourinary system5.79e-0815
large intestine6.47e-0811
anterior region of body6.58e-0862
craniocervical region6.58e-0862
unilaminar epithelium2.76e-07148
immaterial anatomical entity4.12e-07117
epithelium of mucosa6.31e-078


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
ELF1#199774.258097958807543.93848941900192e-050.000735309074778588
EP300#203376.77394172622321.52695018318475e-065.86513976394382e-05
FOS#235378.99795530889442.09217725654467e-071.11881669480936e-05
FOSL2#2355716.93020060456172.50368126508949e-092.11897866810925e-07
FOXA1#3169711.08141974938554.86782131208363e-083.14598013621722e-06
POLR2A#543072.147453176558070.004747636447610280.02234412162372
SIN3A#2594275.408884726815147.3795239773719e-060.000211617272013384
SP1#666775.69838137814095.12280185510121e-060.000157266402982044



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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