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Coexpression cluster:C590: Difference between revisions

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|ontology_enrichment_disease=DOID:2531!2.09e-12!51;DOID:0060083!2.09e-12!51;DOID:1240!7.13e-10!39;DOID:8692!2.07e-07!31
|ontology_enrichment_disease=DOID:2531!2.09e-12!51;DOID:0060083!2.09e-12!51;DOID:1240!7.13e-10!39;DOID:8692!2.07e-07!31
|ontology_enrichment_uberon=UBERON:0002390!1.08e-28!102;UBERON:0003061!1.08e-28!102;UBERON:0002193!1.71e-28!112;UBERON:0002371!2.18e-18!80;UBERON:0007023!2.54e-16!115;UBERON:0002405!1.05e-15!115;UBERON:0001474!2.56e-15!86;UBERON:0003081!7.97e-12!216;UBERON:0004765!4.32e-11!101;UBERON:0001434!4.32e-11!101;UBERON:0000178!6.63e-09!15;UBERON:0000179!6.63e-09!15;UBERON:0000463!6.63e-09!15
|ontology_enrichment_uberon=UBERON:0002390!1.08e-28!102;UBERON:0003061!1.08e-28!102;UBERON:0002193!1.71e-28!112;UBERON:0002371!2.18e-18!80;UBERON:0007023!2.54e-16!115;UBERON:0002405!1.05e-15!115;UBERON:0001474!2.56e-15!86;UBERON:0003081!7.97e-12!216;UBERON:0004765!4.32e-11!101;UBERON:0001434!4.32e-11!101;UBERON:0000178!6.63e-09!15;UBERON:0000179!6.63e-09!15;UBERON:0000463!6.63e-09!15
|pathway_enrichment=3.01170464246961e-06;0.00190640903868326;3;85;Integrin cell surface interactions (Reactome):REACT_13552!1.95641411763581e-05;0.00619205068231735;4;511;Signaling in Immune system (Reactome):REACT_6900
}}
}}

Revision as of 15:04, 13 July 2012


Full id: C590_CD4_CD14CD16_CD14_CD19_Neutrophils_Whole_blood



Phase1 CAGE Peaks

Hg19::chr11:64511549..64511566,-p5@RASGRP2
Hg19::chr12:51717831..51717874,-p3@BIN2
Hg19::chr14:100531713..100531724,+p11@EVL
Hg19::chr15:75074868..75074911,+p2@CSK
Hg19::chr15:75074915..75074938,+p5@CSK
Hg19::chr16:30194916..30194955,+p1@CORO1A
Hg19::chr16:30198468..30198483,+p3@CORO1A
Hg19::chr17:61775799..61775815,-p@chr17:61775799..61775815
-
Hg19::chr17:61776662..61776738,-p2@LIMD2
Hg19::chr17:62097927..62098000,-p1@ICAM2
Hg19::chr19:3178814..3178835,+p2@S1PR4
Hg19::chr19:49838937..49838974,+p@chr19:49838937..49838974
+
Hg19::chr1:167599532..167599568,+p3@RCSD1
Hg19::chr4:83196097..83196106,+p1@ENST00000504996
Hg19::chr7:77428066..77428132,+p2@PHTF2


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
3.01170464246961e-060.00190640903868326385Integrin cell surface interactions (Reactome):REACT_13552
1.95641411763581e-050.006192050682317354511Signaling in Immune system (Reactome):REACT_6900



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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell1.85e-64172
angioblastic mesenchymal cell1.85e-64172
hematopoietic cell3.45e-63182
hematopoietic oligopotent progenitor cell1.36e-60165
hematopoietic multipotent progenitor cell1.36e-60165
leukocyte5.79e-56140
nongranular leukocyte5.37e-48119
hematopoietic lineage restricted progenitor cell1.94e-47124
myeloid cell1.70e-31112
common myeloid progenitor1.70e-31112
lymphocyte1.29e-2653
common lymphoid progenitor1.29e-2653
lymphoid lineage restricted progenitor cell3.09e-2652
myeloid leukocyte2.17e-2476
granulocyte monocyte progenitor cell6.73e-2171
CD14-positive, CD16-negative classical monocyte1.19e-2042
myeloid lineage restricted progenitor cell1.92e-2070
macrophage dendritic cell progenitor2.14e-1965
monopoietic cell3.76e-1963
monocyte3.76e-1963
monoblast3.76e-1963
promonocyte3.76e-1963
classical monocyte1.26e-1645
lymphocyte of B lineage5.10e-1324
pro-B cell5.10e-1324
T cell7.53e-1325
pro-T cell7.53e-1325
mature alpha-beta T cell6.04e-1118
alpha-beta T cell6.04e-1118
immature T cell6.04e-1118
mature T cell6.04e-1118
immature alpha-beta T cell6.04e-1118
B cell2.19e-0914
CD8-positive, alpha-beta T cell2.49e-0711
intermediate monocyte5.84e-079
CD14-positive, CD16-positive monocyte5.84e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.08e-28102
blood island1.08e-28102
hemolymphoid system1.71e-28112
bone marrow2.18e-1880
adult organism2.54e-16115
immune system1.05e-15115
bone element2.56e-1586
lateral plate mesoderm7.97e-12216
skeletal element4.32e-11101
skeletal system4.32e-11101
blood6.63e-0915
haemolymphatic fluid6.63e-0915
organism substance6.63e-0915
Disease
Ontology termp-valuen
hematologic cancer2.09e-1251
immune system cancer2.09e-1251
leukemia7.13e-1039
myeloid leukemia2.07e-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


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.