Personal tools

Coexpression cluster:C2749

From FANTOM5_SSTAR

Revision as of 18:34, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2749_lung_smooth_uterus_cervix_vagina_ovary_kidney



Phase1 CAGE Peaks

Hg19::chr3:64670534..64670545,+p5@ADAMTS9-AS2
Hg19::chr3:64670551..64670629,+p2@ADAMTS9-AS2
Hg19::chr3:64670630..64670642,+p3@ADAMTS9-AS2
Hg19::chr3:64670757..64670798,+p1@ADAMTS9-AS2


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 organism1.63e-44115
neural tube6.86e-2757
neural rod6.86e-2757
future spinal cord6.86e-2757
neural keel6.86e-2757
regional part of brain2.13e-2459
neural plate1.27e-2386
presumptive neural plate1.27e-2386
neurectoderm5.59e-2290
central nervous system6.64e-2282
anterior neural tube2.56e-2142
regional part of nervous system3.86e-2194
nervous system3.86e-2194
brain4.20e-2169
future brain4.20e-2169
regional part of forebrain1.09e-2041
forebrain1.09e-2041
future forebrain1.09e-2041
organism subdivision1.11e-19365
anatomical cluster4.45e-18286
anterior region of body4.84e-18129
craniocervical region4.84e-18129
pre-chordal neural plate5.08e-1861
head6.47e-18123
gray matter1.12e-1734
brain grey matter1.12e-1734
telencephalon2.39e-1734
multi-cellular organism2.89e-17659
anatomical conduit3.47e-17241
regional part of telencephalon6.60e-1733
cerebral hemisphere2.30e-1632
ectoderm-derived structure3.25e-16169
ectoderm1.81e-15173
presumptive ectoderm1.81e-15173
anatomical system1.36e-14625
multi-tissue structure1.95e-14347
anatomical group2.27e-14626
tube2.64e-14194
epithelium1.90e-13309
cell layer3.62e-13312
cerebral cortex6.79e-1325
pallium6.79e-1325
organ7.06e-13511
regional part of cerebral cortex1.50e-1222
neocortex2.06e-1120
embryo5.16e-10612
organ part1.83e-09219
embryonic structure6.04e-09605
developing anatomical structure6.04e-09605
germ layer1.22e-08604
embryonic tissue1.22e-08604
presumptive structure1.22e-08604
epiblast (generic)1.22e-08604
posterior neural tube8.22e-0715
chordal neural plate8.22e-0715


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.