Personal tools

Coexpression cluster:C2822

From FANTOM5_SSTAR

Revision as of 15:36, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2822_Neural_Astrocyte_kidney_mesodermal_H9_cerebellum_Neurons



Phase1 CAGE Peaks

Hg19::chr5:5140200..5140232,-p1@ENST00000512155
Hg19::chr5:5140408..5140419,+p4@ADAMTS16
Hg19::chr5:5140436..5140450,+p2@ADAMTS16
Hg19::chr5:5140462..5140482,+p3@ADAMTS16


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
neural cell1.37e-1125
neuronal stem cell1.17e-108
oligodendrocyte5.69e-097
macroglial cell5.69e-097
astrocyte5.69e-097
oligodendrocyte precursor cell5.69e-097
neuron3.06e-086
neuroblast3.06e-086
electrically signaling cell3.06e-086
neurectodermal cell1.07e-0759
embryonic stem cell2.48e-075
Uber Anatomy
Ontology termp-valuen
central nervous system4.94e-3382
regional part of nervous system3.84e-3294
nervous system3.84e-3294
adult organism8.81e-28115
neural tube3.94e-2557
neural rod3.94e-2557
future spinal cord3.94e-2557
neural keel3.94e-2557
brain2.71e-2469
future brain2.71e-2469
neurectoderm3.62e-2490
neural plate3.74e-2486
presumptive neural plate3.74e-2486
regional part of brain1.36e-2359
cerebral cortex6.05e-2025
pallium6.05e-2025
telencephalon1.96e-1934
gray matter5.58e-1934
brain grey matter5.58e-1934
regional part of telencephalon1.48e-1833
cerebral hemisphere1.82e-1832
ectoderm9.92e-17173
presumptive ectoderm9.92e-17173
regional part of cerebral cortex1.48e-1622
pre-chordal neural plate1.50e-1661
ectoderm-derived structure1.99e-16169
anterior region of body2.84e-16129
craniocervical region2.84e-16129
anterior neural tube3.03e-1642
regional part of forebrain1.26e-1541
forebrain1.26e-1541
future forebrain1.26e-1541
neocortex5.52e-1520
head6.66e-15123
segmental subdivision of hindbrain1.38e-1112
hindbrain1.38e-1112
presumptive hindbrain1.38e-1112
posterior neural tube1.99e-1015
chordal neural plate1.99e-1015
segmental subdivision of nervous system2.08e-1013
regional part of metencephalon1.81e-099
metencephalon1.81e-099
future metencephalon1.81e-099
cerebellum9.70e-086
rhombic lip9.70e-086
embryo2.81e-07612


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
TAF1#687243.343046285745290.008005664898701650.0323131840137392



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.