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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C474_Neutrophils_CD4_CD8_Natural_CD14_Peripheral_CD19
|full_id=C474_Neutrophils_CD4_CD8_Natural_CD14_Peripheral_CD19
|id=C474
|id=C474

Revision as of 17:53, 12 September 2012


Full id: C474_Neutrophils_CD4_CD8_Natural_CD14_Peripheral_CD19



Phase1 CAGE Peaks

Hg19::chr10:112657664..112657669,+p2@MIR4680
Hg19::chr10:27438637..27438641,-p@chr10:27438637..27438641
-
Hg19::chr10:93704937..93704948,+p@chr10:93704937..93704948
+
Hg19::chr11:11868811..11868842,+p@chr11:11868811..11868842
+
Hg19::chr12:62780642..62780650,+p@chr12:62780642..62780650
+
Hg19::chr12:76922107..76922112,-p@chr12:76922107..76922112
-
Hg19::chr15:63822540..63822544,+p@chr15:63822540..63822544
+
Hg19::chr16:11810960..11810964,-p@chr16:11810960..11810964
-
Hg19::chr1:212489954..212489959,+p@chr1:212489954..212489959
+
Hg19::chr1:235393906..235393910,-p@chr1:235393906..235393910
-
Hg19::chr21:38771224..38771228,+p@chr21:38771224..38771228
+
Hg19::chr22:40471183..40471188,+p@chr22:40471183..40471188
+
Hg19::chr2:20532166..20532170,-p@chr2:20532166..20532170
-
Hg19::chr2:42426154..42426168,+p@chr2:42426154..42426168
+
Hg19::chr3:156872939..156872954,-p14@CCNL1
Hg19::chr3:196437710..196437713,-p@chr3:196437710..196437713
-
Hg19::chr5:86704947..86704952,-p@chr5:86704947..86704952
-
Hg19::chr6:13682619..13682628,-p@chr6:13682619..13682628
-
Hg19::chr7:131063657..131063661,+p@chr7:131063657..131063661
+
Hg19::chr9:82197570..82197574,+p@chr9:82197570..82197574
+


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 cell8.94e-31172
angioblastic mesenchymal cell8.94e-31172
leukocyte1.32e-30140
hematopoietic cell1.03e-27182
hematopoietic oligopotent progenitor cell2.78e-27165
hematopoietic multipotent progenitor cell2.78e-27165
nongranular leukocyte7.28e-26119
hematopoietic lineage restricted progenitor cell1.03e-24124
myeloid leukocyte5.89e-1676
myeloid cell2.27e-15112
common myeloid progenitor2.27e-15112
CD14-positive, CD16-negative classical monocyte3.36e-1542
classical monocyte1.95e-1445
myeloid lineage restricted progenitor cell2.42e-1370
macrophage dendritic cell progenitor5.46e-1365
monopoietic cell8.94e-1363
monocyte8.94e-1363
monoblast8.94e-1363
promonocyte8.94e-1363
granulocyte monocyte progenitor cell1.01e-1271
lymphocyte1.24e-1153
common lymphoid progenitor1.24e-1153
lymphoid lineage restricted progenitor cell2.61e-1152
T cell1.88e-0725
pro-T cell1.88e-0725
mature alpha-beta T cell4.55e-0718
alpha-beta T cell4.55e-0718
immature T cell4.55e-0718
mature T cell4.55e-0718
immature alpha-beta T cell4.55e-0718
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.53e-14102
blood island1.53e-14102
hemolymphoid system9.41e-13112
adult organism3.63e-11115
bone marrow5.41e-1080
bone element1.22e-0986
immune system7.35e-08115


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.