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Coexpression cluster:C3129: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3129_Melanocyte_melanoma_occipital_brain_parietal_aorta_Fibroblast
|full_id=C3129_Melanocyte_melanoma_occipital_brain_parietal_aorta_Fibroblast
|id=C3129
|id=C3129

Revision as of 15:59, 12 September 2012


Full id: C3129_Melanocyte_melanoma_occipital_brain_parietal_aorta_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:19734342..19734353,+p@chr11:19734342..19734353
+
Hg19::chr11:19734369..19734391,+p1@NAV2
Hg19::chr11:19734399..19734410,+p4@NAV2


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
non-terminally differentiated cell4.14e-18180
mesodermal cell3.17e-12119
fibroblast3.53e-1175
endothelial cell of vascular tree5.59e-0824
lining cell2.28e-0757
barrier cell2.28e-0757
endothelial cell2.85e-0735
meso-epithelial cell8.75e-0744
Uber Anatomy
Ontology termp-valuen
anatomical cluster3.01e-30286
anatomical conduit3.04e-28241
tube2.21e-26194
cell layer1.92e-25312
epithelium1.68e-24309
neural plate1.88e-2186
presumptive neural plate1.88e-2186
neural tube6.46e-2157
neural rod6.46e-2157
future spinal cord6.46e-2157
neural keel6.46e-2157
regional part of nervous system6.95e-2094
nervous system6.95e-2094
regional part of brain8.90e-1959
neurectoderm9.10e-1990
central nervous system9.25e-1982
ectoderm-derived structure3.02e-18169
organism subdivision3.24e-18365
multi-cellular organism4.19e-17659
multi-tissue structure1.18e-16347
ectoderm1.33e-16173
presumptive ectoderm1.33e-16173
anatomical system1.34e-16625
brain2.03e-1669
future brain2.03e-1669
anatomical group2.36e-16626
pre-chordal neural plate6.36e-1661
head4.14e-15123
anterior neural tube7.06e-1542
regional part of forebrain9.96e-1541
forebrain9.96e-1541
future forebrain9.96e-1541
vasculature2.68e-1479
vascular system2.68e-1479
gray matter3.35e-1434
brain grey matter3.35e-1434
telencephalon5.70e-1434
regional part of telencephalon1.52e-1333
cerebral hemisphere1.62e-1332
organ part1.62e-13219
anterior region of body1.65e-13129
craniocervical region1.65e-13129
epithelial tube7.01e-13118
vessel8.87e-1369
splanchnic layer of lateral plate mesoderm9.05e-1284
embryonic structure5.10e-11605
developing anatomical structure5.10e-11605
adult organism6.10e-11115
cerebral cortex7.07e-1125
pallium7.07e-1125
germ layer8.94e-11604
embryonic tissue8.94e-11604
presumptive structure8.94e-11604
epiblast (generic)8.94e-11604
blood vessel1.21e-1060
epithelial tube open at both ends1.21e-1060
blood vasculature1.21e-1060
vascular cord1.21e-1060
embryo1.82e-10612
circulatory system2.36e-10113
cardiovascular system4.70e-10110
regional part of cerebral cortex1.56e-0922
neocortex3.45e-0920
artery4.11e-0842
arterial blood vessel4.11e-0842
arterial system4.11e-0842
organ2.14e-07511
posterior neural tube2.46e-0715
chordal neural plate2.46e-0715
systemic artery2.68e-0733
systemic arterial system2.68e-0733


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
CCNT2#90536.336201576962630.003930750035764890.018918138386417
E2F1#186934.907389214879320.008460985347239390.0323671971239271
E2F4#1874312.66806031528440.0004917987006298980.00435537729967659
E2F6#187635.017155731697390.00791769806886330.0320472994850992
FOS#235338.99795530889440.001372499272417130.00894939448785494
IRF1#365937.63716375356390.002244692747297240.0127631460058241
MXI1#460139.96157162875930.001011470541259020.00718227983808478
NFYA#4800318.42558069983050.0001598135507814160.00199055067740732
NFYB#4801316.75979325353650.0002123649923296180.00244992681253872
PBX3#5090321.91451268674419.49854535978121e-050.00136060702075187
SP1#666735.69838137814090.005403962701712170.0245469928933593
SUZ12#23512350.11578091106297.93834897779404e-060.000221263204935103
TCF7L2#6934310.77017656313730.0008003181298398380.00611757484903337
USF1#739136.361499277207960.00388404057290560.0189562742835501
YY1#752834.911170749853860.008441455341808260.032799477452402



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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