Personal tools

Coexpression cluster:C1058

From FANTOM5_SSTAR

Revision as of 11:54, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1058_cerebellum_parietal_occipital_pineal_brain_retinoblastoma_temporal



Phase1 CAGE Peaks

Hg19::chr19:10515584..10515599,+p@chr19:10515584..10515599
+
Hg19::chr1:57889966..57889983,-p6@DAB1
Hg19::chr8:9760906..9760907,-p1@ENST00000517675
Hg19::chr8:9763201..9763208,-p7@ENST00000521242
Hg19::chr8:9763221..9763232,-p4@ENST00000521242
Hg19::chr8:9763242..9763268,-p1@ENST00000521242
Hg19::chr8:9763271..9763300,-p3@ENST00000521242
Hg19::chr8:9763301..9763343,-p2@ENST00000521242


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>


Cell Type
Ontology termp-valuen
neuronal stem cell2.51e-078
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.98e-4694
nervous system1.98e-4694
central nervous system8.52e-4482
neural tube3.03e-4057
neural rod3.03e-4057
future spinal cord3.03e-4057
neural keel3.03e-4057
brain4.17e-3469
future brain4.17e-3469
neurectoderm9.57e-3490
regional part of brain1.24e-3359
neural plate6.16e-3386
presumptive neural plate6.16e-3386
regional part of forebrain2.94e-3241
forebrain2.94e-3241
future forebrain2.94e-3241
anterior neural tube5.22e-3142
gray matter6.02e-2834
brain grey matter6.02e-2834
telencephalon6.78e-2834
regional part of telencephalon4.41e-2733
cerebral hemisphere1.15e-2632
pre-chordal neural plate1.02e-2561
ectoderm1.08e-21173
presumptive ectoderm1.08e-21173
cerebral cortex2.09e-2125
pallium2.09e-2125
ectoderm-derived structure8.41e-21169
regional part of cerebral cortex2.66e-2022
neocortex1.14e-1820
head5.11e-18123
anterior region of body2.03e-17129
craniocervical region2.03e-17129
adult organism7.36e-16115
posterior neural tube3.37e-1015
chordal neural plate3.37e-1015
segmental subdivision of nervous system1.19e-0813
segmental subdivision of hindbrain3.71e-0812
hindbrain3.71e-0812
presumptive hindbrain3.71e-0812
basal ganglion4.69e-089
nuclear complex of neuraxis4.69e-089
aggregate regional part of brain4.69e-089
collection of basal ganglia4.69e-089
cerebral subcortex4.69e-089
nucleus of brain5.87e-089
neural nucleus5.87e-089
temporal lobe6.61e-087


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
SUZ12#23512531.32236306941431.68017316924325e-079.26481550277698e-06



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.