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Difference between revisions of "Coexpression cluster:C1532"

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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C1532_CD14_serous_clear_pharyngeal_epidermoid_large_glassy
 
|full_id=C1532_CD14_serous_clear_pharyngeal_epidermoid_large_glassy
 
|id=C1532
 
|id=C1532

Revision as of 05:06, 12 September 2012


Full id: C1532_CD14_serous_clear_pharyngeal_epidermoid_large_glassy



Phase1 CAGE Peaks

  Short description
Hg19::chr6:126240356..126240379,+ p7@NCOA7
Hg19::chr6:126240380..126240430,+ p2@NCOA7
Hg19::chr6:126240442..126240459,+ p4@NCOA7
Hg19::chr6:126240463..126240489,+ p6@NCOA7
Hg19::chr6:126240490..126240501,+ p11@NCOA7
Hg19::chr6:126240542..126240553,+ p14@NCOA7


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
disease_data


Cell Type
Ontology termp-valuen
classical monocyte2.14e-0945
CD14-positive, CD16-negative classical monocyte3.99e-0842
endodermal cell5.98e-0759
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.48e-15169
endoderm1.48e-15169
presumptive endoderm1.48e-15169
digestive system2.21e-14155
digestive tract2.21e-14155
primitive gut2.21e-14155
subdivision of digestive tract4.94e-14129
endodermal part of digestive tract4.94e-14129
mixed endoderm/mesoderm-derived structure7.75e-12130
foregut1.28e-1098
mesoderm2.74e-10448
mesoderm-derived structure2.74e-10448
presumptive mesoderm2.74e-10448
respiratory system1.18e-0772
larynx3.91e-079
primordium5.36e-07168
Disease
Ontology termp-valuen
carcinoma4.35e-10106


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
BCLAF1#9774621.65264761012189.68736949628703e-097.35275568911861e-07
CEBPB#105167.971147625824823.89609159898068e-060.000127078048252949
ELF1#199764.258097958807540.0001677224776288830.00205354839872016
ELK4#2005616.2356816584685.45305335722442e-083.44532026361259e-06
EP300#203366.77394172622321.03454107484288e-050.000269981097739919
FOXA1#3169611.08141974938555.39600313513231e-072.50914145783652e-05
FOXA2#3170624.63046375266524.47024549595265e-093.61913154536278e-07
HDAC2#3066613.41562023662631.71355402088576e-079.4339414015439e-06
HEY1#2346264.040111043105710.0002298968555807510.00253486039907074
HNF4A#3172623.13229036295376.51490260560877e-095.14293207276776e-07
HNF4G#3174628.75342252644681.76556713337063e-091.54304657608448e-07
MAX#414966.452555509007121.3848964723355e-050.00033465340739067
MEF2A#4205618.74323090964412.30307332780908e-081.62961162115889e-06
NFKB1#479065.488063424193843.65870229532191e-050.00070787552615992
PAX5#507966.669565531177831.13557256338955e-050.000290041728901543
POLR2A#543062.147453176558070.01019570676818780.0380731342664033
PRDM1#6396131.8309557774611.88485626211077e-132.86539305907695e-11
SIN3A#2594265.408884726815143.99207083571449e-050.00074345200786588
SP1#666765.69838137814092.91961319085282e-050.00060996495707037
SRF#6722613.79717826216781.44812893459755e-078.1796180530251e-06
STAT1#6772620.70658749719921.2666425711927e-089.3953752480678e-07
STAT2#6773665.26377118644071.28736137622248e-111.59490788578054e-09
STAT3#6774610.51946499715427.37398960627247e-073.27020000207852e-05
TAF1#687263.343046285745290.0007162474284635620.00573783578900867
TBP#690863.706770687096390.000385416472907960.0037813537824363
TCF7L2#6934610.77017656313736.40204410218762e-072.91466034868515e-05
TRIM28#10155618.59052504526252.41896703530258e-081.697812487903e-06



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.