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Coexpression cluster:C1445: Difference between revisions

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|full_id=C1445_Mammary_Keratinocyte_Small_Urothelial_nasal_Gingival_medial
|full_id=C1445_Mammary_Keratinocyte_Small_Urothelial_nasal_Gingival_medial
|id=C1445
|id=C1445
|ontology_enrichment_celltype=CL:0002076!1.03e-23!43;CL:0000066!9.20e-20!254;CL:0000223!1.85e-18!59;CL:0002368!1.62e-15!13;CL:0002159!2.15e-11!13;CL:0002251!7.30e-11!21;CL:0002202!1.19e-09!9;CL:0002632!1.19e-09!9;CL:0000622!9.28e-08!5
|ontology_enrichment_celltype=CL:0002076!2.50e-17!42;CL:0002159!4.93e-13!14;CL:0002621!6.37e-13!3;CL:0002166!2.78e-12!3;CL:0000223!1.43e-11!58;CL:0000066!3.28e-11!253;CL:0000240!5.22e-11!6;CL:0000311!5.22e-11!6;CL:0000079!5.22e-11!6;CL:0000237!5.22e-11!6;CL:0000036!5.22e-11!6;CL:0000357!5.22e-11!6;CL:0000114!5.22e-11!6;CL:0002368!2.36e-10!13;CL:0002327!6.23e-10!4;CL:0002251!1.13e-08!20;CL:0000312!6.03e-08!5;CL:0002077!8.76e-08!34
|ontology_enrichment_disease=DOID:1749!3.11e-12!14;DOID:305!3.51e-10!106
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001004!1.14e-19!72;UBERON:0004119!1.11e-16!169;UBERON:0000925!1.11e-16!169;UBERON:0006595!1.11e-16!169;UBERON:0000065!4.91e-16!53;UBERON:0000072!2.72e-13!46;UBERON:0001007!1.20e-12!155;UBERON:0001555!1.20e-12!155;UBERON:0007026!1.20e-12!155;UBERON:0000077!6.69e-12!130;UBERON:0001557!2.88e-11!19;UBERON:0001041!6.25e-11!98;UBERON:0001950!8.82e-11!20;UBERON:0000064!1.10e-10!219;UBERON:0000062!6.24e-10!511;UBERON:0002619!1.67e-09!22;UBERON:0000166!2.10e-09!21;UBERON:0004921!2.62e-09!129;UBERON:0004185!2.62e-09!129;UBERON:0000200!2.78e-09!6;UBERON:0008947!2.95e-09!38;UBERON:0003258!2.95e-09!38;UBERON:0000161!3.14e-09!35;UBERON:0000153!9.52e-09!129;UBERON:0007811!9.52e-09!129;UBERON:0001737!1.34e-08!9;UBERON:0000033!1.95e-08!123;UBERON:0000956!5.68e-08!25;UBERON:0000203!5.68e-08!25;UBERON:0002050!9.73e-08!605;UBERON:0005423!9.73e-08!605;UBERON:0000922!1.07e-07!612;UBERON:0003729!1.09e-07!5;UBERON:0001869!1.13e-07!32;UBERON:0000165!1.94e-07!28;UBERON:0000930!1.94e-07!28;UBERON:0000923!2.22e-07!604;UBERON:0005291!2.22e-07!604;UBERON:0006598!2.22e-07!604;UBERON:0002532!2.22e-07!604;UBERON:0000924!2.89e-07!173;UBERON:0006601!2.89e-07!173;UBERON:0004121!2.93e-07!169;UBERON:0005911!3.12e-07!82;UBERON:0001893!5.39e-07!34;UBERON:0000481!5.81e-07!347;UBERON:0007196!6.43e-07!14;UBERON:0001558!6.43e-07!14;UBERON:0000467!6.48e-07!625;UBERON:0000480!7.44e-07!626
|ontology_enrichment_uberon=UBERON:0000200!2.71e-15!6;UBERON:0001949!6.37e-13!3;UBERON:0001950!1.44e-12!20;UBERON:0011159!1.61e-12!5;UBERON:0001870!6.66e-12!3;UBERON:0002619!2.46e-11!22;UBERON:0001869!3.61e-11!32;UBERON:0000344!4.41e-11!20;UBERON:0010371!5.94e-11!104;UBERON:0003729!1.84e-10!13;UBERON:0001893!2.09e-10!34;UBERON:0000153!2.46e-10!62;UBERON:0007811!2.46e-10!62;UBERON:0001911!6.23e-10!4;UBERON:0005333!6.23e-10!4;UBERON:0008425!6.23e-10!4;UBERON:0005311!6.23e-10!4;UBERON:0000956!7.63e-10!25;UBERON:0000203!7.63e-10!25;UBERON:0004121!2.28e-09!171;UBERON:0000924!2.28e-09!171;UBERON:0006601!2.28e-09!171;UBERON:0008814!2.30e-09!18;UBERON:0001708!2.56e-09!4;UBERON:0008895!2.56e-09!4;UBERON:0002791!3.55e-09!32;UBERON:0001042!5.66e-09!10;UBERON:0009145!5.66e-09!10;UBERON:0000033!8.99e-09!56;UBERON:0000161!1.07e-08!36;UBERON:0003528!1.52e-08!34;UBERON:0002020!1.52e-08!34;UBERON:0004119!1.67e-08!160;UBERON:0000925!1.67e-08!160;UBERON:0006595!1.67e-08!160;UBERON:0003102!2.44e-08!99;UBERON:0002780!2.59e-08!41;UBERON:0001890!2.59e-08!41;UBERON:0003080!2.59e-08!41;UBERON:0006240!2.59e-08!41;UBERON:0002702!2.60e-08!2;UBERON:0001004!3.32e-08!74;UBERON:0006562!3.94e-08!11;UBERON:0003350!4.63e-08!8;UBERON:0000166!9.74e-08!22;UBERON:0000365!2.28e-07!5;UBERON:0000165!2.68e-07!29;UBERON:0000930!2.68e-07!29
|tf_chipseq_enrich=STAT3#6774;5:8.76622083096187:4.28672496720299e-05:0.000766349313333982
|tf_chipseq_enrich=STAT3#6774;5:8.76622083096187:4.28672496720299e-05:0.000766349313333982
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}}
}}

Revision as of 11:17, 19 October 2012


Full id: C1445_Mammary_Keratinocyte_Small_Urothelial_nasal_Gingival_medial



Phase1 CAGE Peaks

Hg19::chr18:61166381..61166404,-p@chr18:61166381..61166404
-
Hg19::chr6:11807159..11807169,-p19@C6orf105
Hg19::chr6:11807187..11807204,-p8@C6orf105
Hg19::chr6:11807250..11807275,-p10@C6orf105
Hg19::chr6:11807277..11807292,-p13@C6orf105
Hg19::chr6:11807341..11807353,-p14@C6orf105


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>

Uber Anatomy
Ontology termp-valuen
gyrus2.71e-156
gingival epithelium6.37e-133
neocortex1.44e-1220
primary subdivision of cranial skeletal system1.61e-125
frontal cortex6.66e-123
regional part of cerebral cortex2.46e-1122
cerebral hemisphere3.61e-1132
mucosa4.41e-1120
ecto-epithelium5.94e-11104
mouth mucosa1.84e-1013
telencephalon2.09e-1034
anterior region of body2.46e-1062
craniocervical region2.46e-1062
mammary gland6.23e-104
mammary bud6.23e-104
mammary ridge6.23e-104
mammary placode6.23e-104
cerebral cortex7.63e-1025
pallium7.63e-1025
ectoderm-derived structure2.28e-09171
ectoderm2.28e-09171
presumptive ectoderm2.28e-09171
pharyngeal arch system2.30e-0918
jaw skeleton2.56e-094
splanchnocranium2.56e-094
regional part of telencephalon3.55e-0932
chordate pharynx5.66e-0910
pharyngeal region of foregut5.66e-0910
head8.99e-0956
orifice1.07e-0836
brain grey matter1.52e-0834
gray matter1.52e-0834
endoderm-derived structure1.67e-08160
endoderm1.67e-08160
presumptive endoderm1.67e-08160
surface structure2.44e-0899
regional part of forebrain2.59e-0841
forebrain2.59e-0841
anterior neural tube2.59e-0841
future forebrain2.59e-0841
middle frontal gyrus2.60e-082
respiratory system3.32e-0874
pharynx3.94e-0811
epithelium of mucosa4.63e-088
oral opening9.74e-0822
urothelium2.28e-075
mouth2.68e-0729
stomodeum2.68e-0729


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
STAT3#677458.766220830961874.28672496720299e-050.000766349313333982



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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