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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1438_Basophils_CD8_Eosinophils_Natural_CD34_CD133_CD4
|full_id=C1438_Basophils_CD8_Eosinophils_Natural_CD34_CD133_CD4
|id=C1438
|id=C1438

Revision as of 13:59, 12 September 2012


Full id: C1438_Basophils_CD8_Eosinophils_Natural_CD34_CD133_CD4



Phase1 CAGE Peaks

Hg19::chr18:21408652..21408682,+p@chr18:21408652..21408682
+
Hg19::chr19:45947725..45947742,+p@chr19:45947725..45947742
+
Hg19::chr4:80979943..80979995,-p@chr4:80979943..80979995
-
Hg19::chr4:80980200..80980218,+p@chr4:80980200..80980218
+
Hg19::chr7:150063162..150063212,-p@chr7:150063162..150063212
-
Hg19::chr8:37739648..37739679,+p@chr8:37739648..37739679
+


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 cell1.57e-57172
angioblastic mesenchymal cell1.57e-57172
leukocyte9.74e-57140
hematopoietic cell7.58e-55182
hematopoietic oligopotent progenitor cell1.12e-53165
hematopoietic multipotent progenitor cell1.12e-53165
hematopoietic lineage restricted progenitor cell1.79e-45124
nongranular leukocyte2.75e-43119
myeloid cell4.19e-28112
common myeloid progenitor4.19e-28112
CD14-positive, CD16-negative classical monocyte1.67e-2742
myeloid leukocyte1.57e-2576
classical monocyte2.89e-2445
lymphocyte1.43e-2353
common lymphoid progenitor1.43e-2353
lymphoid lineage restricted progenitor cell5.48e-2352
granulocyte monocyte progenitor cell8.08e-2271
myeloid lineage restricted progenitor cell2.43e-2070
macrophage dendritic cell progenitor1.14e-1865
monopoietic cell1.99e-1763
monocyte1.99e-1763
monoblast1.99e-1763
promonocyte1.99e-1763
mesenchymal cell4.17e-17358
connective tissue cell1.11e-15365
motile cell8.35e-14390
T cell2.42e-1225
pro-T cell2.42e-1225
mature alpha-beta T cell2.56e-1118
alpha-beta T cell2.56e-1118
immature T cell2.56e-1118
mature T cell2.56e-1118
immature alpha-beta T cell2.56e-1118
lymphocyte of B lineage1.33e-0924
pro-B cell1.33e-0924
multi fate stem cell7.03e-09430
stem cell8.98e-09444
intermediate monocyte2.03e-089
CD14-positive, CD16-positive monocyte2.03e-089
somatic stem cell2.67e-08436
CD8-positive, alpha-beta T cell4.77e-0811
B cell1.08e-0714
granulocyte1.20e-078
native cell4.96e-07722
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.18e-25102
blood island2.18e-25102
bone marrow3.79e-2180
hemolymphoid system9.08e-21112
bone element5.69e-1986
connective tissue3.54e-15375
skeletal element1.24e-14101
skeletal system1.24e-14101
immune system3.48e-11115


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-050.000742340476652558
BCL11A#53335314.18472755180350.0008080831849424810.00616925436785145
CCNT2#90544.224134384641760.007109805478875810.0296139815908236
EP300#203355.644951438519330.0003688138931814860.00367088098637007
IRF4#3662310.95725634337210.001711753441810940.0106902958625422
MEF2A#420539.371615454822030.002687399947103910.0148032364491343
MEF2C#4208320.6556772463120.0002683563494060410.0028663191629799
MXI1#460146.64104775250620.001288516958039140.00863966503471041
NFKB1#479043.658708949462560.01207927289015230.0438356850958899
SMARCA4#6597252.25530110262930.0005995659215741950.00501024686216093
SPI1#668845.469549005681820.00269730053614140.0148436806140832



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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