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Coexpression cluster:C4273

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Full id: C4273_ductus_epididymis_seminal_parotid_hippocampus_retina_submaxillary



Phase1 CAGE Peaks

Hg19::chr3:121613224..121613254,+p2@SLC15A2
Hg19::chr3:121613265..121613295,+p1@SLC15A2
Hg19::chr3:121613301..121613313,+p3@SLC15A2


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 organism3.29e-69115
neural tube2.77e-4957
neural rod2.77e-4957
future spinal cord2.77e-4957
neural keel2.77e-4957
central nervous system4.89e-4682
regional part of brain7.10e-4459
regional part of nervous system1.06e-4194
nervous system1.06e-4194
anterior neural tube3.10e-4042
neurectoderm9.17e-4090
regional part of forebrain9.85e-4041
forebrain9.85e-4041
future forebrain9.85e-4041
brain9.55e-3969
future brain9.55e-3969
neural plate2.67e-3886
presumptive neural plate2.67e-3886
telencephalon2.80e-3434
gray matter5.12e-3434
brain grey matter5.12e-3434
regional part of telencephalon3.09e-3333
cerebral hemisphere1.71e-3232
ectoderm1.74e-30173
presumptive ectoderm1.74e-30173
anterior region of body2.43e-29129
craniocervical region2.43e-29129
ectoderm-derived structure4.89e-29169
pre-chordal neural plate5.48e-2961
head1.19e-27123
cerebral cortex2.57e-2525
pallium2.57e-2525
regional part of cerebral cortex5.87e-2422
neocortex1.18e-2120
anatomical conduit6.58e-14241
anatomical cluster1.15e-12286
embryo2.85e-12612
organ2.88e-12511
tube2.10e-11194
organ part2.33e-11219
multi-cellular organism8.31e-11659
multi-tissue structure1.06e-10347
basal ganglion1.69e-109
nuclear complex of neuraxis1.69e-109
aggregate regional part of brain1.69e-109
collection of basal ganglia1.69e-109
cerebral subcortex1.69e-109
posterior neural tube3.34e-1015
chordal neural plate3.34e-1015
nucleus of brain4.60e-109
neural nucleus4.60e-109
embryonic structure9.89e-10605
developing anatomical structure9.89e-10605
organism subdivision2.13e-09365
temporal lobe2.33e-097
germ layer2.38e-09604
embryonic tissue2.38e-09604
presumptive structure2.38e-09604
epiblast (generic)2.38e-09604
brainstem2.23e-088
segmental subdivision of nervous system2.39e-0813
telencephalic nucleus2.56e-087
anatomical system3.88e-08625
anatomical group4.74e-08626
segmental subdivision of hindbrain1.12e-0712
hindbrain1.12e-0712
presumptive hindbrain1.12e-0712
gyrus2.06e-076
limbic system3.65e-075
diencephalon7.95e-077
future diencephalon7.95e-077


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
YY1#752834.911170749853860.008441455341808260.0330354537581262



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.