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Coexpression cluster:C2698: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2698_CD19_b_lymphoma_Burkitt_Dendritic_immature_Monocytederived
|full_id=C2698_CD19_b_lymphoma_Burkitt_Dendritic_immature_Monocytederived
|id=C2698
|id=C2698

Revision as of 15:28, 12 September 2012


Full id: C2698_CD19_b_lymphoma_Burkitt_Dendritic_immature_Monocytederived



Phase1 CAGE Peaks

Hg19::chr2:33701352..33701361,+p7@RASGRP3
Hg19::chr2:33701658..33701673,+p2@RASGRP3
Hg19::chr2:33701684..33701702,+p4@RASGRP3
Hg19::chr2:33701707..33701723,+p1@RASGRP3


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
leukocyte3.17e-29140
hematopoietic lineage restricted progenitor cell4.53e-27124
nongranular leukocyte5.53e-26119
hematopoietic stem cell2.74e-25172
angioblastic mesenchymal cell2.74e-25172
hematopoietic oligopotent progenitor cell1.52e-24165
hematopoietic multipotent progenitor cell1.52e-24165
hematopoietic cell2.37e-24182
granulocyte monocyte progenitor cell8.67e-1571
myeloid lineage restricted progenitor cell1.24e-1470
myeloid leukocyte1.58e-1476
macrophage dendritic cell progenitor2.17e-1465
monopoietic cell1.87e-1363
monocyte1.87e-1363
monoblast1.87e-1363
promonocyte1.87e-1363
lymphocyte of B lineage2.82e-1324
pro-B cell2.82e-1324
myeloid cell6.13e-13112
common myeloid progenitor6.13e-13112
CD14-positive, CD16-negative classical monocyte6.45e-1342
lymphocyte8.68e-1253
common lymphoid progenitor8.68e-1253
lymphoid lineage restricted progenitor cell1.73e-1152
classical monocyte1.53e-1045
B cell1.95e-0814
Uber Anatomy
Ontology termp-valuen
adult organism3.30e-31115
hemolymphoid system1.43e-20112
hematopoietic system1.22e-19102
blood island1.22e-19102
neural tube4.13e-1357
neural rod4.13e-1357
future spinal cord4.13e-1357
neural keel4.13e-1357
bone marrow3.82e-1280
immune system5.78e-12115
bone element1.27e-1086
regional part of brain7.20e-1059
anterior neural tube8.66e-1042
regional part of forebrain1.49e-0941
forebrain1.49e-0941
future forebrain1.49e-0941
telencephalon1.76e-0834
gray matter1.82e-0834
brain grey matter1.82e-0834
skeletal element4.11e-08101
skeletal system4.11e-08101
regional part of telencephalon4.73e-0833
central nervous system6.05e-0882
brain6.64e-0869
future brain6.64e-0869
neural plate7.75e-0886
presumptive neural plate7.75e-0886
blood1.32e-0715
haemolymphatic fluid1.32e-0715
organism substance1.32e-0715
cerebral hemisphere1.93e-0732
neurectoderm4.08e-0790
regional part of nervous system5.26e-0794
nervous system5.26e-0794


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
EP300#203335.08045629466740.01144298405398240.0419051794107039
GATA2#2624412.7449317335543.78864877853583e-050.000722708109189961
MAX#414934.839416631755340.01315737137836840.0466396059255817
NFKB1#479045.488063424193840.001102199566301980.00768595983875358
POU2F2#545236.829593043306890.004860473775203740.0227674480000226
SIN3A#2594245.408884726815140.001168172384885160.0079740363205896
SMC3#9126415.04493284493281.95092670935632e-050.000438838756404189
STAT2#6773232.63188559322030.001379588775125520.00898552367230022
TAF1#687243.343046285745290.008005664898701650.0322782548876772
TBP#690843.706770687096390.005296377814784350.0244658499977116
TCF12#693837.975848676639820.003090920396013070.0162855733649081
TCF7L2#6934410.77017656313737.42969445082454e-050.00115606355594408
USF1#739134.771124457905970.01370465887188020.0483221089777276



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.