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Coexpression cluster:C1518: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1518_non_optic_corpus_thalamus_globus_substantia_medulla
|full_id=C1518_non_optic_corpus_thalamus_globus_substantia_medulla
|id=C1518
|id=C1518

Revision as of 14:05, 12 September 2012


Full id: C1518_non_optic_corpus_thalamus_globus_substantia_medulla



Phase1 CAGE Peaks

Hg19::chr4:144257353..144257371,+p@chr4:144257353..144257371
+
Hg19::chr4:144257585..144257614,+p4@GAB1
Hg19::chr4:144257672..144257687,+p2@GAB1
Hg19::chr4:144257996..144258009,+p6@GAB1
Hg19::chr4:144258021..144258052,+p1@GAB1
Hg19::chr4:144258062..144258073,+p9@GAB1


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism3.50e-49115
neural tube5.97e-2557
neural rod5.97e-2557
future spinal cord5.97e-2557
neural keel5.97e-2557
central nervous system1.85e-2382
regional part of brain7.35e-2259
anterior neural tube3.00e-2142
regional part of forebrain4.64e-2141
forebrain4.64e-2141
future forebrain4.64e-2141
brain1.24e-1969
future brain1.24e-1969
regional part of nervous system4.51e-1994
nervous system4.51e-1994
telencephalon4.46e-1834
gray matter5.10e-1834
brain grey matter5.10e-1834
regional part of telencephalon1.85e-1733
cerebral hemisphere9.86e-1732
neural plate1.08e-1486
presumptive neural plate1.08e-1486
neurectoderm2.72e-1390
cerebral cortex9.64e-1325
pallium9.64e-1325
ectoderm-derived structure3.75e-12169
regional part of cerebral cortex1.15e-1122
ectoderm2.38e-11173
presumptive ectoderm2.38e-11173
pre-chordal neural plate4.54e-1161
head8.47e-11123
neocortex1.13e-1020
anterior region of body1.81e-10129
craniocervical region1.81e-10129
anatomical conduit1.01e-09241
organ2.09e-09511
multi-cellular organism8.44e-08659
anatomical group1.48e-07626
anatomical system1.97e-07625
tube5.99e-07194
nucleus of brain7.83e-079
neural nucleus7.83e-079


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
E2F1#186954.089491012399440.001749817597761990.010760080080821
GTF2B#2959315.97191496716210.0005711653715892990.00486795660546881
HEY1#2346264.040111043105710.0002298968555807510.00253432527971269
NR2C2#7182527.17884242103411.5816706961502e-078.84778285137819e-06
POLR2A#543062.147453176558070.01019570676818780.0380636074767745
SMARCB1#659839.126357890578710.002900247150367020.0156788090551882
SPI1#668856.836936257102270.0001449641773974030.00188612354842499
TAF1#687263.343046285745290.0007162474284635620.00573607585164527
TCF12#693835.317232451093210.013367345733860.0472492036788372



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.