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Coexpression cluster:C1431: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;4:16.2385345282024:3.98325915717398e-05:0.00074220803410543!BCL11A#53335;4:18.9129700690714:2.18517293116183e-05:0.000480659805723695!IRF4#3662;4:14.6096751244961:6.03404227507469e-05:0.000991331353101346!MEF2A#4205;4:12.495487273096:0.000111333627719979:0.00154621977997964!NFKB1#4790;4:3.65870894946256:0.0120792728901523:0.0438326389414758!SPI1#6688;5:6.83693625710227:0.000144964177397403:0.00188588860528244
|tf_chipseq_enrich=BATF#10538;4:16.2385345282024:3.98325915717398e-05:0.00074220803410543!BCL11A#53335;4:18.9129700690714:2.18517293116183e-05:0.000480659805723695!IRF4#3662;4:14.6096751244961:6.03404227507469e-05:0.000991331353101346!MEF2A#4205;4:12.495487273096:0.000111333627719979:0.00154621977997964!NFKB1#4790;4:3.65870894946256:0.0120792728901523:0.0438326389414758!SPI1#6688;5:6.83693625710227:0.000144964177397403:0.00188588860528244
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}}
}}

Revision as of 14:53, 26 November 2012


Full id: C1431_CD4_Burkitt_CD8_diffuse_tonsil_spleen_lymphoma



Phase1 CAGE Peaks

Hg19::chr17:37917880..37917904,-p1@AK128436
Hg19::chr17:37921587..37921593,-p@chr17:37921587..37921593
-
Hg19::chr17:37934188..37934202,-p8@IKZF3
Hg19::chr17:37934204..37934241,-p3@IKZF3
Hg19::chr17:37934268..37934277,-p10@IKZF3
Hg19::chr17:37934280..37934299,-p6@IKZF3


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>disease_data<br>

Cell Type
Ontology termp-valuen
lymphocyte2.83e-6953
common lymphoid progenitor2.83e-6953
lymphoid lineage restricted progenitor cell1.61e-6752
nucleate cell4.06e-6655
nongranular leukocyte5.04e-38115
leukocyte1.36e-35136
lymphocyte of B lineage1.15e-3324
pro-B cell1.15e-3324
hematopoietic lineage restricted progenitor cell5.52e-31120
T cell1.08e-2925
pro-T cell1.08e-2925
mature alpha-beta T cell1.53e-2718
alpha-beta T cell1.53e-2718
immature T cell1.53e-2718
mature T cell1.53e-2718
immature alpha-beta T cell1.53e-2718
hematopoietic cell7.89e-26177
hematopoietic stem cell5.04e-25168
angioblastic mesenchymal cell5.04e-25168
hematopoietic oligopotent progenitor cell1.47e-22161
hematopoietic multipotent progenitor cell1.47e-22161
B cell1.42e-1914
CD8-positive, alpha-beta T cell4.85e-1811
CD4-positive, alpha-beta T cell4.60e-106
circulating cell3.50e-096
Uber Anatomy
Ontology termp-valuen
blood6.12e-1915
haemolymphatic fluid6.12e-1915
organism substance6.12e-1915
hemopoietic organ1.39e-107
immune organ1.39e-107
hemolymphoid system2.84e-07108
hematopoietic system2.97e-0798
blood island2.97e-0798
adult organism8.16e-07114
thymus9.97e-074
hemolymphoid system gland9.97e-074
thymic region9.97e-074
pharyngeal gland9.97e-074
thymus primordium9.97e-074
Disease
Ontology termp-valuen
lymphoma9.18e-1210


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
BATF#10538416.23853452820243.98325915717398e-050.00074220803410543
BCL11A#53335418.91297006907142.18517293116183e-050.000480659805723695
IRF4#3662414.60967512449616.03404227507469e-050.000991331353101346
MEF2A#4205412.4954872730960.0001113336277199790.00154621977997964
NFKB1#479043.658708949462560.01207927289015230.0438326389414758
SPI1#668856.836936257102270.0001449641773974030.00188588860528244



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.

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