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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1578_CD14_CD4_Basophils_Eosinophils_Neutrophils_Peripheral_CD14CD16
|full_id=C1578_CD14_CD4_Basophils_Eosinophils_Neutrophils_Peripheral_CD14CD16
|id=C1578
|id=C1578

Revision as of 14:09, 12 September 2012


Full id: C1578_CD14_CD4_Basophils_Eosinophils_Neutrophils_Peripheral_CD14CD16



Phase1 CAGE Peaks

Hg19::chr10:43634422..43634481,-p@chr10:43634422..43634481
-
Hg19::chr12:90257972..90257986,+p@chr12:90257972..90257986
+
Hg19::chr12:90257987..90258016,+p@chr12:90257987..90258016
+
Hg19::chr2:235217704..235217719,+p@chr2:235217704..235217719
+
Hg19::chrX:13105644..13105658,+p@chrX:13105644..13105658
+


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
leukocyte1.51e-56140
hematopoietic stem cell8.72e-51172
angioblastic mesenchymal cell8.72e-51172
hematopoietic cell2.80e-48182
hematopoietic oligopotent progenitor cell2.82e-46165
hematopoietic multipotent progenitor cell2.82e-46165
hematopoietic lineage restricted progenitor cell1.07e-45124
nongranular leukocyte5.52e-44119
CD14-positive, CD16-negative classical monocyte8.32e-3342
myeloid leukocyte8.53e-3176
classical monocyte4.02e-2945
granulocyte monocyte progenitor cell1.05e-2671
myeloid cell2.36e-26112
common myeloid progenitor2.36e-26112
myeloid lineage restricted progenitor cell1.81e-2470
macrophage dendritic cell progenitor4.77e-2465
monopoietic cell8.15e-2363
monocyte8.15e-2363
monoblast8.15e-2363
promonocyte8.15e-2363
lymphoid lineage restricted progenitor cell9.72e-1952
lymphocyte4.97e-1853
common lymphoid progenitor4.97e-1853
mesenchymal cell8.39e-18358
multi fate stem cell1.19e-17430
stem cell4.20e-17444
somatic stem cell7.80e-17436
connective tissue cell1.02e-16365
motile cell5.06e-13390
mature alpha-beta T cell7.62e-1118
alpha-beta T cell7.62e-1118
immature T cell7.62e-1118
mature T cell7.62e-1118
immature alpha-beta T cell7.62e-1118
T cell1.82e-1025
pro-T cell1.82e-1025
native cell6.36e-10722
intermediate monocyte5.72e-099
CD14-positive, CD16-positive monocyte5.72e-099
lymphocyte of B lineage1.34e-0724
pro-B cell1.34e-0724
granulocyte1.40e-078
B cell4.14e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.12e-35102
blood island3.12e-35102
hemolymphoid system1.98e-33112
bone marrow6.63e-2580
bone element2.72e-2186
immune system3.55e-19115
skeletal element1.01e-16101
skeletal system1.01e-16101
connective tissue1.51e-15375
lateral plate mesoderm1.74e-13216
musculoskeletal system4.31e-10167
blood7.65e-0915
haemolymphatic fluid7.65e-0915
organism substance7.65e-0915


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
BCL11A#53335211.34778204144280.01157056933741320.0422834490720493
MAFK#7975210.8402932551320.01263683277337880.0456844535296794
NANOG#79923211.69791139240510.01091164951956080.0402117771409108
SPI1#668846.563458806818180.0009957429636454020.00713953037073748



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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