Personal tools

Coexpression cluster:C4500

From FANTOM5_SSTAR

Revision as of 08:35, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4500_small_frontal_insula_Hep2_non_amygdala_paracentral



Phase1 CAGE Peaks

  Short description
Hg19::chr5:41870475..41870494,- p2@OXCT1
Hg19::chr5:41870495..41870512,- p4@OXCT1
Hg19::chr5:41870518..41870535,- p1@OXCT1


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell8.30e-1552
lymphocyte1.92e-1453
common lymphoid progenitor1.92e-1453
T cell2.12e-0925
pro-T cell2.12e-0925
mature alpha-beta T cell8.72e-0718
alpha-beta T cell8.72e-0718
immature T cell8.72e-0718
mature T cell8.72e-0718
immature alpha-beta T cell8.72e-0718
Uber Anatomy
Ontology termp-valuen
cerebral hemisphere7.19e-1432
telencephalon5.28e-1334
regional part of forebrain7.46e-1341
forebrain7.46e-1341
future forebrain7.46e-1341
gray matter1.32e-1234
brain grey matter1.32e-1234
regional part of telencephalon2.16e-1233
anterior neural tube2.78e-1242
brain3.05e-1269
future brain3.05e-1269
central nervous system3.72e-1282
neural tube3.91e-1257
neural rod3.91e-1257
future spinal cord3.91e-1257
neural keel3.91e-1257
regional part of brain1.23e-1159
cerebral cortex1.40e-1125
pallium1.40e-1125
regional part of cerebral cortex2.21e-1122
regional part of nervous system3.74e-1194
nervous system3.74e-1194
neocortex1.54e-1020
anterior region of body3.58e-09129
craniocervical region3.58e-09129
head1.83e-08123
neural plate4.09e-0886
presumptive neural plate4.09e-0886
pre-chordal neural plate5.74e-0861
larynx1.65e-079
neurectoderm3.20e-0790
ectoderm-derived structure3.25e-07169
upper respiratory tract3.29e-0719


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BRCA1#672320.18423064322380.0001215704860271640.00164422429295402
CCNT2#90536.336201576962630.003930750035764890.0190879064018807
E2F1#186934.907389214879320.008460985347239390.0327159144272616
E2F6#187635.017155731697390.00791769806886330.0323912596895301
HMGN3#932438.178547723350590.001827766942164210.0109067621799045
MXI1#460139.96157162875930.001011470541259020.00722452276422863
MYC#460935.22228187160940.007020843755740150.0295689128561072
NFKB1#479035.488063424193840.006049381815655430.0270597647526657
NRF1#4899312.21027944771090.0005492172401020010.00472913672512267
PAX5#507936.669565531177830.003370290999677260.0173539329347381
POU2F2#545239.106124057742520.001324165192682130.00885028084977147
RFX5#5993312.04791082719510.0005717246050312580.0048616142342338
SMARCB1#6598318.25271578115740.000164397760679890.00203744366057281
SPI1#668838.204323508522730.001810593189410520.0109348604700656
STAT1#6772320.70658749719920.0001125992441046670.00155285256239896
TCF12#6938310.63446490218640.0008313523990202070.00631367169875446
TCF7L2#6934310.77017656313730.0008003181298398380.00616540718170265
YY1#752834.911170749853860.008441455341808260.03308876874505
ZEB1#6935316.88843201754390.0002075486917327580.00243552559728961
ZNF263#1012738.221841637010680.001799043925565870.0109928825498581



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.