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Coexpression cluster:C865

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Full id: C865_CD14_Neutrophils_Dendritic_placenta_cervical_epitheloid_spinal



Phase1 CAGE Peaks

Hg19::chrX:1367460..1367489,+p@chrX:1367460..1367489
+
Hg19::chrX:1368516..1368527,-p@chrX:1368516..1368527
-
Hg19::chrX:1387700..1387717,+p1@CSF2RA
Hg19::chrX:1387721..1387738,+p2@CSF2RA
Hg19::chrX:1393727..1393755,-p@chrX:1393727..1393755
-
Hg19::chrX:1393820..1393849,-p@chrX:1393820..1393849
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Hg19::chrX:1435460..1435487,-p@chrX:1435460..1435487
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Hg19::chrX:1435588..1435602,-p@chrX:1435588..1435602
-
Hg19::chrX:1455478..1455515,+p2@IL3RA
Hg19::chrX:24167737..24167762,-p1@ZFX-AS1


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


p.valueFDRnGenesnPathwayName
8.58567593366187e-050.01358683216501992265Cytokine-cytokine receptor interaction (KEGG):04060
2.92938943019595e-050.006181011697713452155Jak-STAT signaling pathway (KEGG):04630
9.39564536136585e-060.00297372175687229288Hematopoietic cell lineage (KEGG):04640
0.0003198274735665560.03374179846127162511Signaling in Immune system (Reactome):REACT_6900
1.91447319275479e-060.00121186153101378240IL-3 up reg. targets (Netpath):NetPath_15
0.0002017928378747890.02554697327494832406{GRB2,414} (Static Module):NA



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:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.000158559827157831
GO:0004912interleukin-3 receptor activity0.00153064978927681
GO:0019978interleukin-3 binding0.00153064978927681
GO:0004907interleukin receptor activity0.0183575242003379
GO:0019965interleukin binding0.0183575242003379
GO:0004888transmembrane receptor activity0.0230388577844583
GO:0019838growth factor binding0.028372121655368
GO:0019955cytokine binding0.028372121655368
GO:0004872receptor activity0.035793698202971
GO:0005057receptor signaling protein activity0.0387720512564269
GO:0004871signal transducer activity0.0387720512564269
GO:0060089molecular transducer activity0.0387720512564269



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
myeloid lineage restricted progenitor cell3.41e-3666
granulocyte monocyte progenitor cell1.47e-3567
myeloid leukocyte2.02e-3572
monopoietic cell3.39e-3259
monocyte3.39e-3259
monoblast3.39e-3259
promonocyte3.39e-3259
macrophage dendritic cell progenitor5.92e-3161
classical monocyte3.33e-3042
CD14-positive, CD16-negative classical monocyte3.33e-3042
defensive cell1.38e-2848
phagocyte1.38e-2848
myeloid cell5.87e-27108
common myeloid progenitor5.87e-27108
hematopoietic lineage restricted progenitor cell5.81e-17120
leukocyte5.88e-17136
hematopoietic stem cell6.63e-16168
angioblastic mesenchymal cell6.63e-16168
hematopoietic oligopotent progenitor cell1.28e-15161
hematopoietic multipotent progenitor cell1.28e-15161
stuff accumulating cell5.34e-1587
hematopoietic cell1.04e-14177
nongranular leukocyte1.09e-13115
histamine secreting cell3.77e-075
biogenic amine secreting cell3.77e-075
granulocytopoietic cell3.77e-075
mast cell3.77e-075
mast cell progenitor3.77e-075
basophil mast progenitor cell3.77e-075
Uber Anatomy
Ontology termp-valuen
bone marrow1.39e-3076
bone element7.21e-2882
immune system1.02e-2593
skeletal element8.27e-2590
hematopoietic system4.64e-2498
blood island4.64e-2498
skeletal system1.64e-23100
hemolymphoid system3.35e-21108
neural tube3.05e-1456
neural rod3.05e-1456
future spinal cord3.05e-1456
neural keel3.05e-1456
spinal cord8.34e-123
dorsal region element8.34e-123
dorsum8.34e-123
musculoskeletal system2.25e-11167
regional part of nervous system6.71e-1053
regional part of brain6.71e-1053
central nervous system8.59e-1081
regional part of telencephalon5.43e-0932
lateral plate mesoderm5.84e-09203
regional part of cerebral cortex1.01e-0822
neural plate1.36e-0882
presumptive neural plate1.36e-0882
nervous system1.89e-0889
brain grey matter2.25e-0834
gray matter2.25e-0834
telencephalon2.25e-0834
posterior neural tube2.90e-0815
chordal neural plate2.90e-0815
regional part of forebrain3.89e-0841
forebrain3.89e-0841
anterior neural tube3.89e-0841
future forebrain3.89e-0841
neurectoderm4.97e-0886
middle temporal gyrus5.26e-082
cerebral cortex1.42e-0725
pallium1.42e-0725
neocortex2.10e-0720
cerebral hemisphere2.98e-0732
brain5.57e-0768
future brain5.57e-0768


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.