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Coexpression cluster:C489

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Full id: C489_immature_CD14_Natural_Basophils_CD8_CD4_CD34



Phase1 CAGE Peaks

Hg19::chr10:17067939..17067950,+p@chr10:17067939..17067950
+
Hg19::chr10:3845786..3845804,+p@chr10:3845786..3845804
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Hg19::chr11:62310904..62310918,+p@chr11:62310904..62310918
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Hg19::chr11:62310937..62310946,+p@chr11:62310937..62310946
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Hg19::chr11:62310952..62310964,+p@chr11:62310952..62310964
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Hg19::chr11:62310973..62311002,+p@chr11:62310973..62311002
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Hg19::chr11:62321754..62321778,+p@chr11:62321754..62321778
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Hg19::chr12:122228579..122228598,+p@chr12:122228579..122228598
+
Hg19::chr12:72056594..72056607,-p@chr12:72056594..72056607
-
Hg19::chr15:86125585..86125597,+p@chr15:86125585..86125597
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Hg19::chr17:7746945..7746958,+p@chr17:7746945..7746958
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Hg19::chr19:56146912..56146939,-p@chr19:56146912..56146939
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Hg19::chr22:20862211..20862230,-p@chr22:20862211..20862230
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Hg19::chr22:20862231..20862254,-p@chr22:20862231..20862254
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Hg19::chr3:33758833..33758853,+p@chr3:33758833..33758853
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Hg19::chr6:136610032..136610051,+p@chr6:136610032..136610051
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Hg19::chr6:16699696..16699707,-p@chr6:16699696..16699707
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Hg19::chr6:16699727..16699740,-p@chr6:16699727..16699740
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Hg19::chr6:293545..293553,-p@chr6:293545..293553
-


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
classical monocyte1.01e-8542
CD14-positive, CD16-negative classical monocyte1.01e-8542
defensive cell8.75e-7448
phagocyte8.75e-7448
leukocyte7.95e-72136
granulocyte monocyte progenitor cell1.58e-6967
myeloid leukocyte1.69e-6772
macrophage dendritic cell progenitor7.49e-6661
myeloid lineage restricted progenitor cell5.27e-6366
hematopoietic lineage restricted progenitor cell9.34e-63120
monopoietic cell2.02e-6059
monocyte2.02e-6059
monoblast2.02e-6059
promonocyte2.02e-6059
nongranular leukocyte4.59e-60115
hematopoietic stem cell1.11e-55168
angioblastic mesenchymal cell1.11e-55168
hematopoietic cell3.48e-52177
hematopoietic oligopotent progenitor cell4.29e-52161
hematopoietic multipotent progenitor cell4.29e-52161
myeloid cell8.43e-49108
common myeloid progenitor8.43e-49108
stuff accumulating cell5.98e-4187
mesenchymal cell2.24e-21354
connective tissue cell1.08e-20361
motile cell2.69e-18386
multi fate stem cell2.30e-15427
stem cell2.48e-15441
somatic stem cell5.85e-15433
intermediate monocyte5.37e-129
CD14-positive, CD16-positive monocyte5.37e-129
natural killer cell5.64e-113
pro-NK cell5.64e-113
basophil7.54e-113
single nucleate cell1.54e-093
mononuclear cell1.54e-093
CD4-positive, alpha-beta T cell2.16e-086
CD1a-positive Langerhans cell4.97e-082
immature CD1a-positive Langerhans cell4.97e-082
mature alpha-beta T cell1.06e-0718
alpha-beta T cell1.06e-0718
immature T cell1.06e-0718
mature T cell1.06e-0718
immature alpha-beta T cell1.06e-0718
somatic cell2.95e-07588
Uber Anatomy
Ontology termp-valuen
bone marrow4.07e-6076
bone element5.61e-5582
hematopoietic system8.06e-5298
blood island8.06e-5298
skeletal element3.51e-4990
immune system2.92e-4793
hemolymphoid system5.18e-46108
skeletal system3.15e-43100
musculoskeletal system1.08e-21167
connective tissue9.12e-20371
lateral plate mesoderm2.56e-19203
mesoderm1.14e-08315
mesoderm-derived structure1.14e-08315
presumptive mesoderm1.14e-08315


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
CTCF#10664113.103306321253960.0001618769715296470.00201456971277226
CTCFL#14069044.157152496626180.01381538141971840.048596026408473
FOS#235383.788612761639750.0005646531665148650.00481717138193481
HNF4A#317244.869955865884990.00802670606715890.0321841730313667
SMC3#912664.751031424715640.001097208282891840.00766445962523849



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.