Personal tools

Coexpression cluster:C2866

From FANTOM5_SSTAR

Revision as of 13:13, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2866_Fibroblast_Preadipocyte_rhabdomyosarcoma_Myoblast_mesenchymal_Smooth_liposarcoma



Phase1 CAGE Peaks

Hg19::chr6:56819398..56819427,-p13@DST
Hg19::chr6:56819429..56819490,-p10@DST
Hg19::chr6:56819494..56819509,-p28@DST
Hg19::chr6:56819522..56819652,-p3@DST


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
non-terminally differentiated cell1.78e-26180
fibroblast2.16e-1875
skin fibroblast1.53e-1123
Uber Anatomy
Ontology termp-valuen
central nervous system2.56e-2382
brain6.05e-2269
future brain6.05e-2269
neural tube3.15e-2157
neural rod3.15e-2157
future spinal cord3.15e-2157
neural keel3.15e-2157
regional part of nervous system3.44e-2194
nervous system3.44e-2194
regional part of brain7.95e-2059
organism subdivision7.21e-19365
head8.39e-18123
neural plate1.51e-1686
presumptive neural plate1.51e-1686
ectoderm-derived structure3.36e-16169
anterior region of body1.40e-15129
craniocervical region1.40e-15129
ectoderm5.01e-15173
presumptive ectoderm5.01e-15173
regional part of forebrain5.42e-1541
forebrain5.42e-1541
future forebrain5.42e-1541
neurectoderm9.24e-1590
anterior neural tube1.71e-1442
gray matter3.65e-1334
brain grey matter3.65e-1334
telencephalon1.15e-1234
regional part of telencephalon2.59e-1233
cerebral hemisphere4.19e-1232
pre-chordal neural plate4.46e-1061
cerebral cortex1.82e-0925
pallium1.82e-0925
regional part of cerebral cortex4.71e-0922
multi-tissue structure1.21e-08347
neocortex1.81e-0820
somite1.96e-0883
paraxial mesoderm1.96e-0883
presomitic mesoderm1.96e-0883
presumptive segmental plate1.96e-0883
trunk paraxial mesoderm1.96e-0883
presumptive paraxial mesoderm1.96e-0883
posterior neural tube4.04e-0815
chordal neural plate4.04e-0815
anatomical cluster4.80e-08286
skin of body9.65e-0840
tube1.26e-07194
epithelium1.96e-07309
integument2.72e-0745
integumental system2.72e-0745
segmental subdivision of nervous system3.85e-0713
cell layer7.21e-07312
segmental subdivision of hindbrain9.02e-0712
hindbrain9.02e-0712
presumptive hindbrain9.02e-0712
anatomical conduit9.80e-07241


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
CCNT2#90546.336201576962630.0006203100587215640.00513511114638724
E2F1#186944.907389214879320.001724022357361790.0106781621978714
E2F6#187645.017155731697390.00157802193473060.0099907270151145
EBF1#187948.9064668465690.00015887907472010.00199990016689075
EGR1#195844.988179094810140.001615011500076050.0101633035705256
HEY1#2346244.040111043105710.00375304636917980.018657864135128
MAFK#7975427.10073313782991.85228494563408e-066.85752525477058e-05
NFE2#4778477.2042606516292.80776035215453e-081.91910787577661e-06
PAX5#507946.669565531177830.0005052774169483260.00444834090438053
SIN3A#2594245.408884726815140.001168172384885160.0079802953757863
TAF1#687243.343046285745290.008005664898701650.0323269268618737
YY1#752844.911170749853860.00171871838055440.0107062644009735
ZBTB7A#5134135.513931980906920.009038352821081090.0342584209291169



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.