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Coexpression cluster:C4300: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4300_Basophils_Eosinophils_Mast_CD14_CD34_CD4_CD8
|full_id=C4300_Basophils_Eosinophils_Mast_CD14_CD34_CD4_CD8
|gostat_on_coexpression_clusters=GO:0017182!peptidyl-diphthamide metabolic process!0.00147180030613446!285381$GO:0017183!peptidyl-diphthamide biosynthetic process from peptidyl-histidine!0.00147180030613446!285381$GO:0051099!positive regulation of binding!0.00220770045920169!285381$GO:0050709!negative regulation of protein secretion!0.00220770045920169!285381$GO:0018202!peptidyl-histidine modification!0.00323796067349582!285381$GO:0051048!negative regulation of secretion!0.00417010086738098!285381$GO:0050708!regulation of protein secretion!0.00515130107147062!285381$GO:0051098!regulation of binding!0.00515130107147062!285381$GO:0009306!protein secretion!0.00868362180619334!285381$GO:0051046!regulation of secretion!0.00868362180619334!285381$GO:0018193!peptidyl-amino acid modification!0.0161898033674791!285381$GO:0032940!secretion by cell!0.036427057576828!285381$GO:0046903!secretion!0.0434747167350488!285381
|gostat_on_coexpression_clusters=GO:0017182!peptidyl-diphthamide metabolic process!0.00147180030613446!285381$GO:0017183!peptidyl-diphthamide biosynthetic process from peptidyl-histidine!0.00147180030613446!285381$GO:0051099!positive regulation of binding!0.00220770045920169!285381$GO:0050709!negative regulation of protein secretion!0.00220770045920169!285381$GO:0018202!peptidyl-histidine modification!0.00323796067349582!285381$GO:0051048!negative regulation of secretion!0.00417010086738098!285381$GO:0050708!regulation of protein secretion!0.00515130107147062!285381$GO:0051098!regulation of binding!0.00515130107147062!285381$GO:0009306!protein secretion!0.00868362180619334!285381$GO:0051046!regulation of secretion!0.00868362180619334!285381$GO:0018193!peptidyl-amino acid modification!0.0161898033674791!285381$GO:0032940!secretion by cell!0.036427057576828!285381$GO:0046903!secretion!0.0434747167350488!285381

Revision as of 17:21, 12 September 2012


Full id: C4300_Basophils_Eosinophils_Mast_CD14_CD34_CD4_CD8



Phase1 CAGE Peaks

Hg19::chr3:16306114..16306133,-p5@DPH3
Hg19::chr3:53925835..53925860,-p2@ENST00000487571
Hg19::chr3:53925863..53925933,-p1@ENST00000485414
p1@ENST00000487571
p1@ENST00000488746


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:0017182peptidyl-diphthamide metabolic process0.00147180030613446
GO:0017183peptidyl-diphthamide biosynthetic process from peptidyl-histidine0.00147180030613446
GO:0051099positive regulation of binding0.00220770045920169
GO:0050709negative regulation of protein secretion0.00220770045920169
GO:0018202peptidyl-histidine modification0.00323796067349582
GO:0051048negative regulation of secretion0.00417010086738098
GO:0050708regulation of protein secretion0.00515130107147062
GO:0051098regulation of binding0.00515130107147062
GO:0009306protein secretion0.00868362180619334
GO:0051046regulation of secretion0.00868362180619334
GO:0018193peptidyl-amino acid modification0.0161898033674791
GO:0032940secretion by cell0.036427057576828
GO:0046903secretion0.0434747167350488



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
leukocyte3.37e-40140
hematopoietic lineage restricted progenitor cell3.80e-33124
nongranular leukocyte5.55e-30119
hematopoietic stem cell1.64e-25172
angioblastic mesenchymal cell1.64e-25172
myeloid leukocyte5.64e-2576
hematopoietic cell1.02e-24182
hematopoietic oligopotent progenitor cell4.24e-23165
hematopoietic multipotent progenitor cell4.24e-23165
CD14-positive, CD16-negative classical monocyte2.30e-2242
classical monocyte4.14e-2145
myeloid lineage restricted progenitor cell4.36e-2170
granulocyte monocyte progenitor cell3.75e-2071
macrophage dendritic cell progenitor1.37e-1865
monopoietic cell1.67e-1763
monocyte1.67e-1763
monoblast1.67e-1763
promonocyte1.67e-1763
myeloid cell2.99e-12112
common myeloid progenitor2.99e-12112
lymphocyte4.10e-1153
common lymphoid progenitor4.10e-1153
lymphoid lineage restricted progenitor cell6.55e-1152
mesenchymal cell1.93e-09358
connective tissue cell1.71e-08365
mature alpha-beta T cell1.37e-0718
alpha-beta T cell1.37e-0718
immature T cell1.37e-0718
mature T cell1.37e-0718
immature alpha-beta T cell1.37e-0718
motile cell5.34e-07390
T cell7.44e-0725
pro-T cell7.44e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.28e-24102
blood island4.28e-24102
hemolymphoid system1.43e-19112
bone marrow4.44e-1980
bone element5.07e-1786
adult organism1.30e-15115
skeletal element4.77e-15101
skeletal system4.77e-15101
immune system3.55e-13115
blood2.39e-0815
haemolymphatic fluid2.39e-0815
organism substance2.39e-0815
connective tissue3.73e-07375


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
ATF3#467322.46317452600878.81932387510763e-050.00129894424790913
BCLAF1#9774214.43509840674790.006201147435546130.0273936907630912
BRCA1#672213.45615376214920.007119807716084560.0296367316883282
CCNT2#90536.336201576962630.003930750035764890.0190604328621622
E2F1#186934.907389214879320.008460985347239390.0326602915686108
E2F6#187635.017155731697390.00791769806886330.0323405869847868
EGR1#195834.988179094810140.008056488137383440.032161591796506
ELF1#199734.258097958807540.01295179875054610.0463768268834053
ELK4#2005316.2356816584680.0002336043955745990.00256113893233419
GABPB1#255337.067683836182170.002832212825417420.0154542045597581
GATA1#2623313.56030814380040.0004009615963782630.00388748868957941
IRF1#365937.63716375356390.002244692747297240.0128456693608206
JUN#3725312.51282919233630.0005103313992726250.00445341753080161
MAFF#23764237.54357099329680.0009344774015560320.0067709092091793
MAFK#7975218.06715542521990.003983674744936810.0191155987450703
NANOG#79923219.49651898734180.003427255648501020.0174553375925972
NFE2#4778251.4695071010860.0004987653528392110.00440698432192677
NFKB1#479035.488063424193840.006049381815655430.027028508553807
NFYA#4800212.28372046655370.008516011403724430.0324872599259808
NFYB#4801211.17319550235760.01025467135054530.0381473774240284
PAX5#507936.669565531177830.003370290999677260.017336837990213
SETDB1#9869226.8800174520070.001814468907964410.010897143086768
SIN3A#2594235.408884726815140.006318961977991520.0277638228868093
SIX5#147912317.0867153554590.0002004060546325010.00240107926348099
SMARCB1#6598212.16847718743830.008675002221921740.033003371596069
SP1#666735.69838137814090.005403962701712170.024727675280587
SRF#6722313.79717826216780.0003806615025800190.00375835759765122
THAP1#55145331.36914460285133.23800758564397e-050.000648340249687635
YY1#752834.911170749853860.008441455341808260.0330404060429154



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.