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Coexpression cluster:C1518

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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 organism1.48e-47114
neural tube1.35e-2456
neural rod1.35e-2456
future spinal cord1.35e-2456
neural keel1.35e-2456
central nervous system3.28e-2381
regional part of nervous system9.38e-2353
regional part of brain9.38e-2353
regional part of forebrain2.79e-2141
forebrain2.79e-2141
anterior neural tube2.79e-2141
future forebrain2.79e-2141
nervous system3.77e-2089
brain8.09e-2068
future brain8.09e-2068
telencephalon3.13e-1834
brain grey matter3.17e-1834
gray matter3.17e-1834
regional part of telencephalon5.64e-1732
cerebral hemisphere6.96e-1732
neural plate1.85e-1582
presumptive neural plate1.85e-1582
organ system subdivision2.89e-14223
neurectoderm3.02e-1486
cerebral cortex6.17e-1325
pallium6.17e-1325
ectoderm-derived structure2.00e-12171
ectoderm2.00e-12171
presumptive ectoderm2.00e-12171
ecto-epithelium7.09e-12104
regional part of cerebral cortex7.39e-1222
pre-chordal neural plate2.25e-1161
neocortex8.17e-1120
organ8.39e-11503
anatomical conduit7.32e-10240
multi-cellular organism1.58e-09656
structure with developmental contribution from neural crest1.17e-08132
anatomical group2.63e-08625
anatomical system3.14e-08624
anatomical cluster8.61e-08373
tube4.00e-07192
embryonic structure5.96e-07564
neural nucleus7.77e-079
nucleus of brain7.77e-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.