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Coexpression cluster:C4319

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Full id: C4319_extraskeletal_thyroid_pituitary_cerebellum_aorta_parietal_colon



Phase1 CAGE Peaks

Hg19::chr3:2140383..2140394,+p13@CNTN4
Hg19::chr3:2140446..2140470,+p4@CNTN4
Hg19::chr3:2140476..2140505,+p3@CNTN4


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 organism4.40e-59115
neural tube1.55e-3757
neural rod1.55e-3757
future spinal cord1.55e-3757
neural keel1.55e-3757
neurectoderm1.60e-3790
neural plate2.55e-3686
presumptive neural plate2.55e-3686
regional part of brain2.73e-3059
regional part of forebrain1.47e-2941
forebrain1.47e-2941
future forebrain1.47e-2941
brain1.84e-2969
future brain1.84e-2969
central nervous system2.44e-2982
anterior neural tube1.58e-2842
regional part of nervous system6.78e-2894
nervous system6.78e-2894
cerebral hemisphere4.13e-2632
pre-chordal neural plate8.28e-2661
telencephalon1.35e-2534
anterior region of body2.10e-25129
craniocervical region2.10e-25129
gray matter2.57e-2534
brain grey matter2.57e-2534
regional part of telencephalon1.56e-2433
head1.12e-23123
ectoderm2.28e-23173
presumptive ectoderm2.28e-23173
regional part of cerebral cortex4.60e-2322
ectoderm-derived structure3.29e-22169
neocortex6.64e-2220
cerebral cortex6.57e-2125
pallium6.57e-2125
organ2.88e-15511
organ part2.12e-14219
multi-tissue structure5.23e-14347
embryo2.19e-12612
embryonic structure2.28e-10605
developing anatomical structure2.28e-10605
epithelium4.16e-10309
multi-cellular organism4.55e-10659
posterior neural tube5.47e-1015
chordal neural plate5.47e-1015
germ layer6.44e-10604
embryonic tissue6.44e-10604
presumptive structure6.44e-10604
epiblast (generic)6.44e-10604
cell layer9.41e-10312
anatomical cluster1.62e-09286
organism subdivision2.57e-09365
tube2.77e-09194
temporal lobe6.60e-097
anatomical conduit8.26e-09241
anatomical system4.06e-08625
anatomical group4.92e-08626
gyrus1.32e-076
segmental subdivision of hindbrain2.10e-0712
hindbrain2.10e-0712
presumptive hindbrain2.10e-0712
large intestine4.10e-0711
colon5.18e-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


No analysis results for this cluster

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.