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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.10390816741244,0.122518063916678,0.168334756349589,0,0.477900580372591,0.201181785145201,0.159286732874341,0.104078526590485,0.358108758021183,0.429876822043327,0.0661163340840885,0.105969788764328,0.198548821842283,0,0,0,0.127081471617318,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C388_CD4_CD8_cord_Peripheral_Natural_Whole_thymus
|full_id=C388_CD4_CD8_cord_Peripheral_Natural_Whole_thymus
|gostat_on_coexpression_clusters=GO:0007218!neuropeptide signaling pathway!0.00508860167908128!342372;5367$GO:0030354!melanin-concentrating hormone activity!0.0103013890731043!5367$GO:0007025!beta-tubulin folding!0.0103013890731043!6904$GO:0007021!tubulin folding!0.0139052377329709!6904$GO:0051087!chaperone binding!0.0197722629543939!6904$GO:0007631!feeding behavior!0.0380792453878901!5367
|gostat_on_coexpression_clusters=GO:0007218!neuropeptide signaling pathway!0.00508860167908128!342372;5367$GO:0030354!melanin-concentrating hormone activity!0.0103013890731043!5367$GO:0007025!beta-tubulin folding!0.0103013890731043!6904$GO:0007021!tubulin folding!0.0139052377329709!6904$GO:0051087!chaperone binding!0.0197722629543939!6904$GO:0007631!feeding behavior!0.0380792453878901!5367

Revision as of 16:53, 12 September 2012


Full id: C388_CD4_CD8_cord_Peripheral_Natural_Whole_thymus



Phase1 CAGE Peaks

Hg19::chr10:102270916..102270937,-p@chr10:102270916..102270937
-
Hg19::chr10:63977682..63977689,-p@chr10:63977682..63977689
-
Hg19::chr10:63977707..63977724,-p@chr10:63977707..63977724
-
Hg19::chr10:6625733..6625740,+p2@ENST00000449648
Hg19::chr11:114189327..114189369,+p@chr11:114189327..114189369
+
Hg19::chr12:102591576..102591596,-p1@PMCH
Hg19::chr14:23006547..23006583,+p1@TRAJ7
Hg19::chr16:72033758..72033771,-p1@PKD1L3
Hg19::chr17:80851254..80851295,+p3@TBCD
Hg19::chr20:39768553..39768594,+p@chr20:39768553..39768594
+
Hg19::chr2:28203275..28203307,+p@chr2:28203275..28203307
+
Hg19::chr2:28203353..28203364,+p@chr2:28203353..28203364
+
Hg19::chr2:28837237..28837245,-p@chr2:28837237..28837245
-
Hg19::chr3:105895690..105895701,+p@chr3:105895690..105895701
+
Hg19::chr3:194209056..194209074,+p@chr3:194209056..194209074
+
Hg19::chr4:82353730..82353737,-p@chr4:82353730..82353737
-
Hg19::chr4:82353753..82353763,-p@chr4:82353753..82353763
-
Hg19::chr5:66118077..66118092,+p@chr5:66118077..66118092
+
Hg19::chr6:130455835..130455839,-p@chr6:130455835..130455839
-
Hg19::chr6:149639812..149639830,+p12@TAB2
Hg19::chr6:149639840..149639869,+p9@TAB2
Hg19::chr6:29803155..29803158,+p@chr6:29803155..29803158
+
Hg19::chr6:37249918..37249929,+p@chr6:37249918..37249929
+
Hg19::chr6:37249933..37249954,+p@chr6:37249933..37249954
+
Hg19::chrX:49122760..49122762,-p@chrX:49122760..49122762
-
Hg19::chrX:49122911..49122916,-p@chrX:49122911..49122916
-
Hg19::chrX:49122952..49122962,-p@chrX:49122952..49122962
-


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

GO IDGO nameFDR corrected p-value
GO:0007218neuropeptide signaling pathway0.00508860167908128
GO:0030354melanin-concentrating hormone activity0.0103013890731043
GO:0007025beta-tubulin folding0.0103013890731043
GO:0007021tubulin folding0.0139052377329709
GO:0051087chaperone binding0.0197722629543939
GO:0007631feeding behavior0.0380792453878901



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
leukocyte1.70e-31140
hematopoietic stem cell9.84e-31172
angioblastic mesenchymal cell9.84e-31172
hematopoietic cell5.71e-30182
nongranular leukocyte1.44e-28119
hematopoietic oligopotent progenitor cell1.83e-27165
hematopoietic multipotent progenitor cell1.83e-27165
hematopoietic lineage restricted progenitor cell1.20e-26124
lymphoid lineage restricted progenitor cell9.98e-1952
lymphocyte1.05e-1853
common lymphoid progenitor1.05e-1853
T cell4.86e-1825
pro-T cell4.86e-1825
mature alpha-beta T cell1.10e-1418
alpha-beta T cell1.10e-1418
immature T cell1.10e-1418
mature T cell1.10e-1418
immature alpha-beta T cell1.10e-1418
myeloid cell7.40e-11112
common myeloid progenitor7.40e-11112
macrophage dendritic cell progenitor2.81e-1065
myeloid leukocyte1.07e-0976
monopoietic cell1.90e-0963
monocyte1.90e-0963
monoblast1.90e-0963
promonocyte1.90e-0963
CD8-positive, alpha-beta T cell2.08e-0911
myeloid lineage restricted progenitor cell7.63e-0970
granulocyte monocyte progenitor cell7.85e-0971
CD14-positive, CD16-negative classical monocyte1.94e-0742
classical monocyte2.15e-0745
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.01e-17102
blood island9.01e-17102
hemolymphoid system2.39e-16112
blood6.13e-1115
haemolymphatic fluid6.13e-1115
organism substance6.13e-1115
adult organism1.61e-07115
bone marrow3.29e-0780


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

No analysis results for this cluster

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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