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Coexpression cluster:C3488: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3488_thymus_CD4_giant_Peripheral_CD8_CD19_Dendritic
|full_id=C3488_thymus_CD4_giant_Peripheral_CD8_CD19_Dendritic
|id=C3488
|id=C3488

Revision as of 16:25, 12 September 2012


Full id: C3488_thymus_CD4_giant_Peripheral_CD8_CD19_Dendritic



Phase1 CAGE Peaks

Hg19::chr15:43478059..43478094,-p@chr15:43478059..43478094
-
Hg19::chr3:195163834..195163851,-p6@ACAP2
Hg19::chr3:195163852..195163868,-p5@ACAP2


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>


Uber Anatomy
Ontology termp-valuen
adult organism3.19e-20115
regional part of nervous system1.56e-1594
nervous system1.56e-1594
central nervous system3.09e-1482
neural tube7.67e-1457
neural rod7.67e-1457
future spinal cord7.67e-1457
neural keel7.67e-1457
brain1.00e-1269
future brain1.00e-1269
regional part of forebrain1.95e-1241
forebrain1.95e-1241
future forebrain1.95e-1241
anterior neural tube4.57e-1242
regional part of brain1.55e-1159
telencephalon1.73e-1034
gray matter2.23e-1034
brain grey matter2.23e-1034
regional part of telencephalon3.99e-1033
cerebral hemisphere6.42e-1032
neurectoderm2.48e-0890
regional part of cerebral cortex5.40e-0822
neocortex6.21e-0820
blood2.25e-0715
haemolymphatic fluid2.25e-0715
organism substance2.25e-0715
neural plate2.27e-0786
presumptive neural plate2.27e-0786
cerebral cortex5.42e-0725
pallium5.42e-0725


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
ATF3#467214.97544968400580.005768294540793880.025951361831049
ELF1#199734.258097958807540.01295179875054610.0461190900002824
GABPB1#255337.067683836182170.002832212825417420.0153850762131369
HSF1#32972109.5271111111110.0001105984013436550.00153682629562665
IRF3#3661231.32130147432640.001339514673320110.00887506013873498
NFYA#4800212.28372046655370.008516011403724430.0324659140351734
NFYB#4801211.17319550235760.01025467135054530.0381161513694782
PBX3#5090214.60967512449610.006056122473217890.0268188337423848
SIX5#147912211.3911435703060.009873820081429030.0370659536136144
SP2#6668217.43568699589640.004273568481769740.0203116054731751
SREBF1#6720231.33723296032550.00133816265136180.00887398369074705
STAT1#6772213.80439166479950.006770931708444080.0287482452515729
TFAP2A#7020211.01242291536330.01054990655215560.039005299150403



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.