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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C662_Mast_CD8_Natural_Basophils_CD4_Peripheral_Dendritic
|full_id=C662_Mast_CD8_Natural_Basophils_CD4_Peripheral_Dendritic
|gostat_on_coexpression_clusters=GO:0030854!positive regulation of granulocyte differentiation!0.00596079123984457!861$GO:0030852!regulation of granulocyte differentiation!0.00596079123984457!861$GO:0030851!granulocyte differentiation!0.0149002234807402!861$GO:0002763!positive regulation of myeloid leukocyte differentiation!0.0149002234807402!861$GO:0004691!cAMP-dependent protein kinase activity!0.0190706017369349!11214$GO:0045766!positive regulation of angiogenesis!0.0193657290530936!861$GO:0004690!cyclic nucleotide-dependent protein kinase activity!0.0193657290530936!11214$GO:0045639!positive regulation of myeloid cell differentiation!0.0193657290530936!861$GO:0002761!regulation of myeloid leukocyte differentiation!0.0198611167149153!861$GO:0002573!myeloid leukocyte differentiation!0.0357342245604695!861$GO:0045637!regulation of myeloid cell differentiation!0.0368127436255965!861$GO:0045765!regulation of angiogenesis!0.0377105745980246!861$GO:0045597!positive regulation of cell differentiation!0.0430427686180983!861$GO:0019992!diacylglycerol binding!0.0446283343177092!11214$GO:0031404!chloride ion binding!0.0446283343177092!861$GO:0043168!anion binding!0.0446283343177092!861$GO:0051094!positive regulation of developmental process!0.0475867330910966!861$GO:0006968!cellular defense response!0.0475867330910966!10219$GO:0030099!myeloid cell differentiation!0.0482057734703268!861
|gostat_on_coexpression_clusters=GO:0030854!positive regulation of granulocyte differentiation!0.00596079123984457!861$GO:0030852!regulation of granulocyte differentiation!0.00596079123984457!861$GO:0030851!granulocyte differentiation!0.0149002234807402!861$GO:0002763!positive regulation of myeloid leukocyte differentiation!0.0149002234807402!861$GO:0004691!cAMP-dependent protein kinase activity!0.0190706017369349!11214$GO:0045766!positive regulation of angiogenesis!0.0193657290530936!861$GO:0004690!cyclic nucleotide-dependent protein kinase activity!0.0193657290530936!11214$GO:0045639!positive regulation of myeloid cell differentiation!0.0193657290530936!861$GO:0002761!regulation of myeloid leukocyte differentiation!0.0198611167149153!861$GO:0002573!myeloid leukocyte differentiation!0.0357342245604695!861$GO:0045637!regulation of myeloid cell differentiation!0.0368127436255965!861$GO:0045765!regulation of angiogenesis!0.0377105745980246!861$GO:0045597!positive regulation of cell differentiation!0.0430427686180983!861$GO:0019992!diacylglycerol binding!0.0446283343177092!11214$GO:0031404!chloride ion binding!0.0446283343177092!861$GO:0043168!anion binding!0.0446283343177092!861$GO:0051094!positive regulation of developmental process!0.0475867330910966!861$GO:0006968!cellular defense response!0.0475867330910966!10219$GO:0030099!myeloid cell differentiation!0.0482057734703268!861

Revision as of 18:19, 12 September 2012


Full id: C662_Mast_CD8_Natural_Basophils_CD4_Peripheral_Dendritic



Phase1 CAGE Peaks

Hg19::chr12:9142131..9142229,+p1@KLRG1
Hg19::chr12:9142239..9142262,+p4@KLRG1
Hg19::chr12:9142310..9142328,+p5@KLRG1
Hg19::chr12:9142330..9142341,+p@chr12:9142330..9142341
+
Hg19::chr12:9144805..9144867,+p3@KLRG1
Hg19::chr15:86126120..86126165,+p3@AKAP13
Hg19::chr16:85588893..85588910,-p@chr16:85588893..85588910
-
Hg19::chr1:23430065..23430077,+p@chr1:23430065..23430077
+
Hg19::chr21:36421147..36421193,-p10@RUNX1
Hg19::chr21:36421347..36421380,-p8@RUNX1
Hg19::chr4:151749436..151749449,-p@chr4:151749436..151749449
-
Hg19::chr4:151749450..151749479,-p@chr4:151749450..151749479
-
Hg19::chr4:151749484..151749504,-p@chr4:151749484..151749504
-


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:0030854positive regulation of granulocyte differentiation0.00596079123984457
GO:0030852regulation of granulocyte differentiation0.00596079123984457
GO:0030851granulocyte differentiation0.0149002234807402
GO:0002763positive regulation of myeloid leukocyte differentiation0.0149002234807402
GO:0004691cAMP-dependent protein kinase activity0.0190706017369349
GO:0045766positive regulation of angiogenesis0.0193657290530936
GO:0004690cyclic nucleotide-dependent protein kinase activity0.0193657290530936
GO:0045639positive regulation of myeloid cell differentiation0.0193657290530936
GO:0002761regulation of myeloid leukocyte differentiation0.0198611167149153
GO:0002573myeloid leukocyte differentiation0.0357342245604695
GO:0045637regulation of myeloid cell differentiation0.0368127436255965
GO:0045765regulation of angiogenesis0.0377105745980246
GO:0045597positive regulation of cell differentiation0.0430427686180983
GO:0019992diacylglycerol binding0.0446283343177092
GO:0031404chloride ion binding0.0446283343177092
GO:0043168anion binding0.0446283343177092
GO:0051094positive regulation of developmental process0.0475867330910966
GO:0006968cellular defense response0.0475867330910966
GO:0030099myeloid cell differentiation0.0482057734703268



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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell5.60e-57172
angioblastic mesenchymal cell5.60e-57172
hematopoietic cell2.87e-53182
hematopoietic oligopotent progenitor cell1.01e-52165
hematopoietic multipotent progenitor cell1.01e-52165
leukocyte6.29e-47140
hematopoietic lineage restricted progenitor cell2.28e-39124
nongranular leukocyte1.48e-36119
myeloid cell5.09e-33112
common myeloid progenitor5.09e-33112
myeloid leukocyte1.64e-2476
granulocyte monocyte progenitor cell3.48e-2171
myeloid lineage restricted progenitor cell5.62e-2170
macrophage dendritic cell progenitor1.14e-1765
monopoietic cell3.15e-1763
monocyte3.15e-1763
monoblast3.15e-1763
promonocyte3.15e-1763
lymphoid lineage restricted progenitor cell3.95e-1752
lymphocyte4.47e-1753
common lymphoid progenitor4.47e-1753
CD14-positive, CD16-negative classical monocyte2.86e-1542
classical monocyte1.25e-1345
T cell6.09e-1325
pro-T cell6.09e-1325
mature alpha-beta T cell2.09e-1218
alpha-beta T cell2.09e-1218
immature T cell2.09e-1218
mature T cell2.09e-1218
immature alpha-beta T cell2.09e-1218
mesenchymal cell5.33e-12358
connective tissue cell1.67e-10365
CD8-positive, alpha-beta T cell1.20e-0811
motile cell8.69e-08390
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.13e-28102
blood island6.13e-28102
hemolymphoid system2.91e-26112
bone marrow2.43e-1880
immune system1.14e-15115
bone element1.78e-1586
adult organism2.43e-13115
lateral plate mesoderm7.61e-12216
skeletal element8.70e-12101
skeletal system8.70e-12101
connective tissue1.08e-09375
blood4.74e-0915
haemolymphatic fluid4.74e-0915
organism substance4.74e-0915
Disease
Ontology termp-valuen
hematologic cancer1.08e-0851
immune system cancer1.08e-0851
leukemia2.11e-0839
myeloid leukemia1.81e-0731


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#10538611.24206236567866.38699523402909e-060.000188326198545106
FOS#235353.460752041882460.01011210325939170.0378285676734585
GATA2#262476.862655548836762.05065762260648e-050.000454517469115871
IRF4#366246.742926980536660.002221995594476970.0127759853496796
JUN#372576.737677257411872.31332287642027e-050.000504913537911089
SPI1#668863.786610850087410.002614000338510870.0144530457596345



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.