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Coexpression cluster:C2224: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487077591519205!CEBPB#1051;3:5.97836071936861:0.00715383248472697:0.0297203194587056!JUN#3725;3:9.38462189425225:0.00191899450203047:0.0112828839046085!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386738140250739!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249223599490314!STAT1#6772;3:15.5299406228994:0.00043408865517555:0.00404928412449797!TAL1#6886;3:22.4014625080802:0.000146275639593017:0.00188906659125202
|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487077591519205!CEBPB#1051;3:5.97836071936861:0.00715383248472697:0.0297203194587056!JUN#3725;3:9.38462189425225:0.00191899450203047:0.0112828839046085!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386738140250739!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249223599490314!STAT1#6772;3:15.5299406228994:0.00043408865517555:0.00404928412449797!TAL1#6886;3:22.4014625080802:0.000146275639593017:0.00188906659125202
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}}
}}

Revision as of 15:22, 26 November 2012


Full id: C2224_Natural_Neutrophils_Eosinophils_Basophils_CD8_acute_NK



Phase1 CAGE Peaks

Hg19::chr12:57873329..57873429,-p2@ARHGAP9
Hg19::chr2:103035024..103035052,+p4@IL18RAP
Hg19::chr2:103035056..103035093,+p3@IL18RAP
Hg19::chr2:103035102..103035117,+p2@IL18RAP


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
hematopoietic stem cell2.25e-45168
angioblastic mesenchymal cell2.25e-45168
leukocyte2.72e-44136
hematopoietic cell2.70e-42177
hematopoietic oligopotent progenitor cell6.32e-42161
hematopoietic multipotent progenitor cell6.32e-42161
hematopoietic lineage restricted progenitor cell1.29e-31120
myeloid cell3.11e-30108
common myeloid progenitor3.11e-30108
nongranular leukocyte5.36e-30115
myeloid leukocyte3.94e-2872
granulocyte monocyte progenitor cell2.43e-2167
myeloid lineage restricted progenitor cell2.14e-1966
classical monocyte7.45e-1942
CD14-positive, CD16-negative classical monocyte7.45e-1942
mature alpha-beta T cell7.87e-1918
alpha-beta T cell7.87e-1918
immature T cell7.87e-1918
mature T cell7.87e-1918
immature alpha-beta T cell7.87e-1918
macrophage dendritic cell progenitor1.15e-1861
monopoietic cell2.79e-1759
monocyte2.79e-1759
monoblast2.79e-1759
promonocyte2.79e-1759
defensive cell4.41e-1648
phagocyte4.41e-1648
T cell1.55e-1425
pro-T cell1.55e-1425
CD8-positive, alpha-beta T cell2.90e-1311
granulocyte6.26e-118
lymphoid lineage restricted progenitor cell6.51e-1152
lymphocyte1.57e-1053
common lymphoid progenitor1.57e-1053
nucleate cell8.25e-1055
blood cell8.02e-0911
mesenchymal cell1.75e-07354
connective tissue cell7.40e-07361
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.84e-3098
blood island1.84e-3098
hemolymphoid system6.18e-28108
immune system1.07e-1893
bone marrow5.23e-1776
adult organism9.62e-17114
bone element1.08e-1482
blood3.68e-1215
haemolymphatic fluid3.68e-1215
organism substance3.68e-1215
skeletal element3.89e-1290
skeletal system3.49e-10100
lateral plate mesoderm2.58e-08203


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
CCNT2#90534.752151182721970.01386206996689490.0487077591519205
CEBPB#105135.978360719368610.007153832484726970.0297203194587056
JUN#372539.384621894252250.001918994502030470.0112828839046085
JUND#372735.245997956403270.01043432751748420.0386738140250739
SPI1#668848.204323508522730.000220661881527680.00249223599490314
STAT1#6772315.52994062289940.000434088655175550.00404928412449797
TAL1#6886322.40146250808020.0001462756395930170.00188906659125202



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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