Personal tools

Coexpression cluster:C1856

From FANTOM5_SSTAR

Revision as of 17:43, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1856_brain_parietal_temporal_occipital_duodenum_Fibroblast_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr1:34286163..34286166,-p@chr1:34286163..34286166
-
Hg19::chr1:34630742..34630755,-p3@CSMD2
Hg19::chr1:34630758..34630772,-p2@CSMD2
Hg19::chr1:34630820..34630844,-p1@CSMD2
Hg19::chr1:34630978..34630987,-p5@CSMD2


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>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
central nervous system5.13e-3382
regional part of nervous system1.03e-3094
nervous system1.03e-3094
neural tube3.42e-3057
neural rod3.42e-3057
future spinal cord3.42e-3057
neural keel3.42e-3057
brain5.14e-2669
future brain5.14e-2669
regional part of brain1.19e-2559
neurectoderm2.88e-2590
organism subdivision4.77e-25365
neural plate5.80e-2586
presumptive neural plate5.80e-2586
regional part of forebrain4.19e-2341
forebrain4.19e-2341
future forebrain4.19e-2341
ectoderm3.35e-22173
presumptive ectoderm3.35e-22173
gray matter4.78e-2234
brain grey matter4.78e-2234
anterior neural tube5.62e-2242
telencephalon7.97e-2234
ectoderm-derived structure1.10e-21169
regional part of telencephalon3.33e-2133
cerebral hemisphere6.74e-2132
pre-chordal neural plate3.60e-1761
head5.98e-17123
cerebral cortex9.85e-1725
pallium9.85e-1725
anterior region of body4.71e-16129
craniocervical region4.71e-16129
regional part of cerebral cortex2.46e-1522
tube3.23e-15194
cell layer4.83e-15312
adult organism5.30e-15115
epithelium1.02e-14309
neocortex3.08e-1420
anatomical conduit8.73e-13241
multi-cellular organism2.09e-12659
integument7.71e-1145
integumental system7.71e-1145
anatomical cluster2.76e-10286
dermomyotome4.39e-1070
anatomical system9.98e-10625
anatomical group1.50e-09626
skin of body1.53e-0940
posterior neural tube2.57e-0915
chordal neural plate2.57e-0915
multilaminar epithelium6.78e-0982
multi-tissue structure7.42e-09347
organ part7.78e-09219
somite1.13e-0883
paraxial mesoderm1.13e-0883
presomitic mesoderm1.13e-0883
presumptive segmental plate1.13e-0883
trunk paraxial mesoderm1.13e-0883
presumptive paraxial mesoderm1.13e-0883
systemic artery1.85e-0833
systemic arterial system1.85e-0833
artery2.50e-0842
arterial blood vessel2.50e-0842
arterial system2.50e-0842
segmental subdivision of nervous system5.92e-0813
segmental subdivision of hindbrain1.91e-0712
hindbrain1.91e-0712
presumptive hindbrain1.91e-0712
skeletal muscle tissue2.07e-0761
striated muscle tissue2.07e-0761
myotome2.07e-0761
embryo2.45e-07612
muscle tissue5.63e-0763
musculature5.63e-0763
musculature of body5.63e-0763
nucleus of brain9.18e-079
neural nucleus9.18e-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.