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Coexpression cluster:C2698: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;3:5.0804562946674:0.0114429840539824:0.0419051794107039!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000722708109189961!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466396059255817!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768595983875358!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227674480000226!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.0079740363205896!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000438838756404189!STAT2#6773;2:32.6318855932203:0.00137958877512552:0.00898552367230022!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322782548876772!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244658499977116!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162855733649081!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115606355594408!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483221089777276
|tf_chipseq_enrich=EP300#2033;3:5.0804562946674:0.0114429840539824:0.0419051794107039!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000722708109189961!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466396059255817!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768595983875358!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227674480000226!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.0079740363205896!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000438838756404189!STAT2#6773;2:32.6318855932203:0.00137958877512552:0.00898552367230022!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322782548876772!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244658499977116!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162855733649081!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115606355594408!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483221089777276
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}}
}}

Revision as of 15:40, 26 November 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
leukocyte9.28e-34136
hematopoietic lineage restricted progenitor cell4.99e-32120
nongranular leukocyte1.14e-30115
hematopoietic stem cell1.22e-28168
angioblastic mesenchymal cell1.22e-28168
hematopoietic oligopotent progenitor cell4.79e-28161
hematopoietic multipotent progenitor cell4.79e-28161
hematopoietic cell7.47e-28177
myeloid lineage restricted progenitor cell5.71e-1966
granulocyte monocyte progenitor cell8.80e-1967
macrophage dendritic cell progenitor8.85e-1961
myeloid leukocyte2.57e-1872
defensive cell1.09e-1748
phagocyte1.09e-1748
monopoietic cell1.11e-1759
monocyte1.11e-1759
monoblast1.11e-1759
promonocyte1.11e-1759
myeloid cell1.31e-15108
common myeloid progenitor1.31e-15108
classical monocyte3.82e-1442
CD14-positive, CD16-negative classical monocyte3.82e-1442
lymphocyte of B lineage3.29e-1324
pro-B cell3.29e-1324
nucleate cell4.81e-1355
lymphocyte3.85e-1253
common lymphoid progenitor3.85e-1253
lymphoid lineage restricted progenitor cell7.33e-1252
B cell1.97e-0814
stuff accumulating cell1.02e-0787
Uber Anatomy
Ontology termp-valuen
adult organism5.67e-30114
hemolymphoid system8.57e-25108
hematopoietic system5.45e-2498
blood island5.45e-2498
immune system1.61e-1893
bone marrow1.27e-1576
bone element1.55e-1382
neural tube9.57e-1256
neural rod9.57e-1256
future spinal cord9.57e-1256
neural keel9.57e-1256
regional part of nervous system2.40e-1053
regional part of brain2.40e-1053
skeletal element1.14e-0990
regional part of forebrain3.17e-0941
forebrain3.17e-0941
anterior neural tube3.17e-0941
future forebrain3.17e-0941
skeletal system4.23e-09100
telencephalon1.96e-0834
brain grey matter2.06e-0834
gray matter2.06e-0834
blood8.44e-0815
haemolymphatic fluid8.44e-0815
organism substance8.44e-0815
neural plate1.07e-0782
presumptive neural plate1.07e-0782
regional part of telencephalon1.77e-0732
cerebral hemisphere2.08e-0732
brain3.83e-0768
future brain3.83e-0768
central nervous system5.33e-0781
neurectoderm5.55e-0786


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.