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Coexpression cluster:C3921

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Full id: C3921_aorta_gall_heart_skin_pituitary_lung_testicular



Phase1 CAGE Peaks

Hg19::chr1:202162920..202162945,+p1@LGR6
Hg19::chr1:202163015..202163027,+p8@LGR6
Hg19::chr1:202163046..202163067,+p4@LGR6


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 organism1.07e-51115
neural tube1.24e-2257
neural rod1.24e-2257
future spinal cord1.24e-2257
neural keel1.24e-2257
neural plate4.65e-1886
presumptive neural plate4.65e-1886
regional part of brain2.13e-1759
central nervous system1.06e-1682
neurectoderm1.59e-1690
brain2.35e-1569
future brain2.35e-1569
posterior neural tube3.57e-1315
chordal neural plate3.57e-1315
regional part of nervous system4.08e-1394
nervous system4.08e-1394
anterior neural tube3.00e-1242
regional part of forebrain1.98e-1141
forebrain1.98e-1141
future forebrain1.98e-1141
segmental subdivision of hindbrain1.59e-1012
hindbrain1.59e-1012
presumptive hindbrain1.59e-1012
ectoderm-derived structure3.69e-10169
anterior region of body1.06e-09129
craniocervical region1.06e-09129
ectoderm1.64e-09173
presumptive ectoderm1.64e-09173
segmental subdivision of nervous system1.92e-0913
head5.16e-09123
anatomical conduit9.17e-09241
pre-chordal neural plate1.46e-0861
tube3.95e-08194
diencephalon4.22e-087
future diencephalon4.22e-087
brainstem7.00e-088
male reproductive organ1.55e-0711
regional part of metencephalon1.67e-079
metencephalon1.67e-079
future metencephalon1.67e-079
anatomical cluster2.83e-07286
gray matter3.25e-0734
brain grey matter3.25e-0734
organ4.60e-07511
neocortex6.97e-0720
regional part of cerebral cortex7.00e-0722
telencephalon9.17e-0734


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
CTCF#1066435.360256373075030.0064925092527670.0279582391394769
SUZ12#23512350.11578091106297.93834897779404e-060.000222510260035382



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.