Personal tools

Coexpression cluster:C407: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 3: Line 3:
|gostat_on_coexpression_clusters=GO:0009756!carbohydrate mediated signaling!0.0133550151197745!64581$GO:0006910!phagocytosis, recognition!0.0133550151197745!64581$GO:0042832!defense response to protozoan!0.0133550151197745!64581$GO:0001562!response to protozoan!0.0133550151197745!64581$GO:0005885!Arp2/3 protein complex!0.0149567362972983!10096$GO:0008329!pattern recognition receptor activity!0.0213636212234457!64581$GO:0009743!response to carbohydrate stimulus!0.0274626613699662!64581$GO:0042287!MHC protein binding!0.0296603415103792!64581$GO:0046966!thyroid hormone receptor binding!0.0296603415103792!221037$GO:0005102!receptor binding!0.033105752264889!221037;64581$GO:0008037!cell recognition!0.0336600330303587!64581$GO:0030027!lamellipodium!0.0336600330303587!10096$GO:0006909!phagocytosis!0.0336600330303587!64581$GO:0035257!nuclear hormone receptor binding!0.040537128657825!221037$GO:0051427!hormone receptor binding!0.040537128657825!221037$GO:0010033!response to organic substance!0.0413311162716758!64581$GO:0031252!leading edge!0.0426417620285896!10096$GO:0051213!dioxygenase activity!0.0426417620285896!221037$GO:0016702!oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen!0.0426417620285896!221037$GO:0016701!oxidoreductase activity, acting on single donors with incorporation of molecular oxygen!0.0426417620285896!221037$GO:0042110!T cell activation!0.0497223462987851!64581
|gostat_on_coexpression_clusters=GO:0009756!carbohydrate mediated signaling!0.0133550151197745!64581$GO:0006910!phagocytosis, recognition!0.0133550151197745!64581$GO:0042832!defense response to protozoan!0.0133550151197745!64581$GO:0001562!response to protozoan!0.0133550151197745!64581$GO:0005885!Arp2/3 protein complex!0.0149567362972983!10096$GO:0008329!pattern recognition receptor activity!0.0213636212234457!64581$GO:0009743!response to carbohydrate stimulus!0.0274626613699662!64581$GO:0042287!MHC protein binding!0.0296603415103792!64581$GO:0046966!thyroid hormone receptor binding!0.0296603415103792!221037$GO:0005102!receptor binding!0.033105752264889!221037;64581$GO:0008037!cell recognition!0.0336600330303587!64581$GO:0030027!lamellipodium!0.0336600330303587!10096$GO:0006909!phagocytosis!0.0336600330303587!64581$GO:0035257!nuclear hormone receptor binding!0.040537128657825!221037$GO:0051427!hormone receptor binding!0.040537128657825!221037$GO:0010033!response to organic substance!0.0413311162716758!64581$GO:0031252!leading edge!0.0426417620285896!10096$GO:0051213!dioxygenase activity!0.0426417620285896!221037$GO:0016702!oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen!0.0426417620285896!221037$GO:0016701!oxidoreductase activity, acting on single donors with incorporation of molecular oxygen!0.0426417620285896!221037$GO:0042110!T cell activation!0.0497223462987851!64581
|id=C407
|id=C407
|ontology_enrichment_celltype=CL:0000738!7.47e-49!140;CL:0000037!4.29e-43!172;CL:0000566!4.29e-43!172;CL:0002032!5.28e-40!165;CL:0000837!5.28e-40!165;CL:0002031!9.94e-40!124;CL:0000988!3.81e-39!182;CL:0002087!1.14e-38!119;CL:0000766!4.39e-30!76;CL:0002057!1.14e-26!42;CL:0000763!4.73e-25!112;CL:0000049!4.73e-25!112;CL:0000557!5.35e-25!71;CL:0000839!6.06e-25!70;CL:0002009!3.43e-24!65;CL:0000860!3.16e-23!45;CL:0002194!3.35e-23!63;CL:0000576!3.35e-23!63;CL:0000040!3.35e-23!63;CL:0000559!3.35e-23!63;CL:0000542!2.06e-13!53;CL:0000051!2.06e-13!53;CL:0000838!2.69e-13!52
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!3.29e-30!102;UBERON:0003061!3.29e-30!102;UBERON:0002193!1.49e-28!112;UBERON:0002371!3.82e-21!80;UBERON:0001474!6.10e-20!86;UBERON:0002405!1.08e-16!115;UBERON:0004765!3.79e-14!101;UBERON:0001434!3.79e-14!101;UBERON:0007023!2.76e-11!115;UBERON:0000178!1.13e-08!15;UBERON:0000179!1.13e-08!15;UBERON:0000463!1.13e-08!15
}}
}}

Revision as of 14:44, 21 May 2012


Full id: C407_Neutrophils_CD14_Eosinophils_Peripheral_CD19_CD4_Natural



Phase1 CAGE Peaks

Hg19::chr10:14641848..14641853,-p@chr10:14641848..14641853
-
Hg19::chr10:65028665..65028674,-p17@JMJD1C
Hg19::chr10:70848483..70848488,+p@chr10:70848483..70848488
+
Hg19::chr11:78029412..78029415,-p@chr11:78029412..78029415
-
Hg19::chr11:78127822..78127826,-p@chr11:78127822..78127826
-
Hg19::chr12:10279509..10279514,-p4@CLEC7A
Hg19::chr12:65057642..65057645,+p@chr12:65057642..65057645
+
Hg19::chr12:90064720..90064735,-p@chr12:90064720..90064735
-
Hg19::chr14:100842126..100842137,+p@chr14:100842126..100842137
+
Hg19::chr14:70149688..70149690,+p@chr14:70149688..70149690
+
Hg19::chr15:51047821..51047824,-p@chr15:51047821..51047824
-
Hg19::chr17:49187745..49187750,-p@chr17:49187745..49187750
-
Hg19::chr19:10389255..10389259,+p@chr19:10389255..10389259
+
Hg19::chr20:48315901..48315905,-p@chr20:48315901..48315905
-
Hg19::chr20:5590491..5590495,-p@chr20:5590491..5590495
-
Hg19::chr20:5590556..5590620,-p@chr20:5590556..5590620
-
Hg19::chr2:114691822..114691837,+p3@ACTR3
Hg19::chr2:114692625..114692632,+p@chr2:114692625..114692632
+
Hg19::chr2:131867907..131867911,+p@chr2:131867907..131867911
+
Hg19::chr2:145263063..145263073,-p@chr2:145263063..145263073
-
Hg19::chr2:201984578..201984581,+p@chr2:201984578..201984581
+
Hg19::chr2:37876585..37876589,-p@chr2:37876585..37876589
-
Hg19::chr2:64367919..64367920,-p@chr2:64367919..64367920
-
Hg19::chr4:103423374..103423399,+p@chr4:103423374..103423399
+
Hg19::chr5:90679281..90679304,+p@chr5:90679281..90679304
+


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:0009756carbohydrate mediated signaling0.0133550151197745
GO:0006910phagocytosis, recognition0.0133550151197745
GO:0042832defense response to protozoan0.0133550151197745
GO:0001562response to protozoan0.0133550151197745
GO:0005885Arp2/3 protein complex0.0149567362972983
GO:0008329pattern recognition receptor activity0.0213636212234457
GO:0009743response to carbohydrate stimulus0.0274626613699662
GO:0042287MHC protein binding0.0296603415103792
GO:0046966thyroid hormone receptor binding0.0296603415103792
GO:0005102receptor binding0.033105752264889
GO:0008037cell recognition0.0336600330303587
GO:0030027lamellipodium0.0336600330303587
GO:0006909phagocytosis0.0336600330303587
GO:0035257nuclear hormone receptor binding0.040537128657825
GO:0051427hormone receptor binding0.040537128657825
GO:0010033response to organic substance0.0413311162716758
GO:0031252leading edge0.0426417620285896
GO:0051213dioxygenase activity0.0426417620285896
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0426417620285896
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0426417620285896
GO:0042110T cell activation0.0497223462987851



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
leukocyte7.47e-49140
hematopoietic stem cell4.29e-43172
angioblastic mesenchymal cell4.29e-43172
hematopoietic oligopotent progenitor cell5.28e-40165
hematopoietic multipotent progenitor cell5.28e-40165
hematopoietic lineage restricted progenitor cell9.94e-40124
hematopoietic cell3.81e-39182
nongranular leukocyte1.14e-38119
myeloid leukocyte4.39e-3076
CD14-positive, CD16-negative classical monocyte1.14e-2642
myeloid cell4.73e-25112
common myeloid progenitor4.73e-25112
granulocyte monocyte progenitor cell5.35e-2571
myeloid lineage restricted progenitor cell6.06e-2570
macrophage dendritic cell progenitor3.43e-2465
classical monocyte3.16e-2345
monopoietic cell3.35e-2363
monocyte3.35e-2363
monoblast3.35e-2363
promonocyte3.35e-2363
lymphocyte2.06e-1353
common lymphoid progenitor2.06e-1353
lymphoid lineage restricted progenitor cell2.69e-1352
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.29e-30102
blood island3.29e-30102
hemolymphoid system1.49e-28112
bone marrow3.82e-2180
bone element6.10e-2086
immune system1.08e-16115
skeletal element3.79e-14101
skeletal system3.79e-14101
adult organism2.76e-11115
blood1.13e-0815
haemolymphatic fluid1.13e-0815
organism substance1.13e-0815


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.