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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1704_CD4_Dendritic_CD8_CD19_Natural_Basophils_Eosinophils
|full_id=C1704_CD4_Dendritic_CD8_CD19_Natural_Basophils_Eosinophils
|gostat_on_coexpression_clusters=GO:0007023!post-chaperonin tubulin folding pathway!0.00147180030613446!6903$GO:0007025!beta-tubulin folding!0.00183975038266808!6903$GO:0007021!tubulin folding!0.0022077004592017!6903$GO:0051087!chaperone binding!0.00294360061226893!6903$GO:0005874!microtubule!0.0423142588013658!6903$GO:0006457!protein folding!0.0423142588013658!6903
|gostat_on_coexpression_clusters=GO:0007023!post-chaperonin tubulin folding pathway!0.00147180030613446!6903$GO:0007025!beta-tubulin folding!0.00183975038266808!6903$GO:0007021!tubulin folding!0.0022077004592017!6903$GO:0051087!chaperone binding!0.00294360061226893!6903$GO:0005874!microtubule!0.0423142588013658!6903$GO:0006457!protein folding!0.0423142588013658!6903

Revision as of 14:18, 12 September 2012


Full id: C1704_CD4_Dendritic_CD8_CD19_Natural_Basophils_Eosinophils



Phase1 CAGE Peaks

Hg19::chr13:28024374..28024401,+p@chr13:28024374..28024401
+
Hg19::chr15:50647015..50647042,-p2@FLJ10038
Hg19::chr2:55845029..55845079,+p@chr2:55845029..55845079
+
Hg19::chr6:42713792..42713847,-p1@TBCC
Hg19::chrX:106960429..106960457,+p@chrX:106960429..106960457
+


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:0007023post-chaperonin tubulin folding pathway0.00147180030613446
GO:0007025beta-tubulin folding0.00183975038266808
GO:0007021tubulin folding0.0022077004592017
GO:0051087chaperone binding0.00294360061226893
GO:0005874microtubule0.0423142588013658
GO:0006457protein folding0.0423142588013658



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
hematopoietic stem cell1.84e-42172
angioblastic mesenchymal cell1.84e-42172
hematopoietic cell1.64e-41182
leukocyte2.13e-40140
hematopoietic oligopotent progenitor cell1.69e-38165
hematopoietic multipotent progenitor cell1.69e-38165
hematopoietic lineage restricted progenitor cell7.46e-32124
nongranular leukocyte1.30e-30119
myeloid cell3.23e-19112
common myeloid progenitor3.23e-19112
lymphocyte9.00e-1953
common lymphoid progenitor9.00e-1953
lymphoid lineage restricted progenitor cell1.37e-1852
myeloid leukocyte1.86e-1676
classical monocyte6.37e-1445
granulocyte monocyte progenitor cell7.98e-1471
CD14-positive, CD16-negative classical monocyte1.39e-1342
myeloid lineage restricted progenitor cell5.08e-1370
mature alpha-beta T cell4.91e-1218
alpha-beta T cell4.91e-1218
immature T cell4.91e-1218
mature T cell4.91e-1218
immature alpha-beta T cell4.91e-1218
macrophage dendritic cell progenitor8.44e-1265
monopoietic cell3.89e-1163
monocyte3.89e-1163
monoblast3.89e-1163
promonocyte3.89e-1163
T cell3.71e-1025
pro-T cell3.71e-1025
B cell9.23e-0914
CD8-positive, alpha-beta T cell3.60e-0811
lymphocyte of B lineage4.94e-0824
pro-B cell4.94e-0824
mesenchymal cell4.77e-07358
connective tissue cell7.26e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.74e-18102
blood island3.74e-18102
hemolymphoid system1.93e-17112
bone marrow2.14e-1180
bone element1.87e-1086
immune system1.75e-09115
skeletal element6.02e-07101
skeletal system6.02e-07101
blood6.70e-0715
haemolymphatic fluid6.70e-0715
organism substance6.70e-0715


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
CCNT2#90545.068961261570110.002709998091280770.0148931535811025
CHD2#110636.206413700470110.007774550126275590.0319483077174148
E2F1#186943.925911371903460.007214984547106360.0298721812136865
EGR1#195843.990543275848110.0067800983001440.0287614413634744
ELF1#199743.406478367046030.01235066105299550.0447304050252729
GABPB1#255345.654147068945740.001776696502096670.0109061012097375
GTF2B#2959212.77753197372970.00919936089559720.0347866342943363
GTF2F1#2962410.19172870140610.000177833889427640.00215837229261282
MAX#414945.16204440720570.002526309009485180.013996349617613
MEF2C#4208216.52454179704960.005579850077982050.0252416495124688
MYC#460944.177825497287520.005691969036823440.0256743350711239
NFKB1#479055.488063424193840.0002008162847462320.00238900238781315
POU2F2#545247.284899246194020.0006631223288743860.00542332285867752
REST#597835.790017229676810.009468788694433940.0356930203731317
SP1#666744.558705102512720.00407573565781680.019478595907506
SPI1#668846.563458806818180.0009957429636454020.00714100112477938
TAF1#687253.343046285745290.002394600090870310.0135242071647417
TAF7#687936.859841642954350.005843286407019040.0262423990136599
TAL1#6886211.94744667097610.0104757781809920.0388040360859948
TBP#690853.706770687096390.001428755106721120.00918093610969343
YY1#752843.928936599883080.007193866269917620.0298367896177247



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.