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Coexpression cluster:C1015

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Full id: C1015_occipital_neuroectodermal_temporal_parietal_duodenum_brain_small



Phase1 CAGE Peaks

Hg19::chr12:45269119..45269133,-p@chr12:45269119..45269133
-
Hg19::chr12:45269871..45269882,-p5@NELL2
Hg19::chr12:45269952..45269963,-p6@NELL2
Hg19::chr12:45269964..45269979,-p2@NELL2
Hg19::chr12:45269990..45270001,-p4@NELL2
Hg19::chr12:45270077..45270143,-p1@NELL2
Hg19::chr12:45270151..45270162,-p3@NELL2
Hg19::chr17:44091602..44091622,+p@chr17:44091602..44091622
+


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>disease_data<br>


Cell Type
Ontology termp-valuen
mature alpha-beta T cell1.72e-1318
alpha-beta T cell1.72e-1318
immature T cell1.72e-1318
mature T cell1.72e-1318
immature alpha-beta T cell1.72e-1318
CD8-positive, alpha-beta T cell3.89e-1311
T cell2.18e-0825
pro-T cell2.18e-0825
neuron2.02e-076
neuroblast2.02e-076
electrically signaling cell2.02e-076
neuronal stem cell3.50e-078
Uber Anatomy
Ontology termp-valuen
nervous system1.56e-4389
central nervous system1.85e-4381
neural tube3.78e-4256
neural rod3.78e-4256
future spinal cord3.78e-4256
neural keel3.78e-4256
regional part of nervous system1.82e-4153
regional part of brain1.82e-4153
adult organism6.64e-39114
neurectoderm7.00e-3886
regional part of forebrain4.90e-3541
forebrain4.90e-3541
anterior neural tube4.90e-3541
future forebrain4.90e-3541
brain6.31e-3568
future brain6.31e-3568
neural plate1.81e-3482
presumptive neural plate1.81e-3482
pre-chordal neural plate4.72e-3161
cerebral hemisphere3.14e-2932
telencephalon6.89e-2934
regional part of cerebral cortex1.21e-2822
brain grey matter2.06e-2834
gray matter2.06e-2834
regional part of telencephalon7.98e-2732
neocortex2.78e-2620
ecto-epithelium2.11e-25104
ectoderm-derived structure2.15e-25171
ectoderm2.15e-25171
presumptive ectoderm2.15e-25171
cerebral cortex2.80e-2425
pallium2.80e-2425
organ system subdivision1.25e-19223
structure with developmental contribution from neural crest1.24e-16132
temporal lobe1.89e-096
anatomical cluster2.89e-09373
gyrus1.02e-086
posterior neural tube1.63e-0815
chordal neural plate1.63e-0815
segmental subdivision of hindbrain9.37e-0812
hindbrain9.37e-0812
presumptive hindbrain9.37e-0812
parietal lobe1.20e-075
occipital lobe1.39e-075
diencephalon1.67e-077
future diencephalon1.67e-077
limbic system2.19e-075
segmental subdivision of nervous system5.65e-0713
brainstem9.15e-076
Disease
Ontology termp-valuen
neuroectodermal tumor8.81e-0710


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
CTBP2#1488215.6792500848320.006675872541887170.0284046872159274



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.