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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C675_Eosinophils_CD14_Natural_CD8_Neutrophils_Basophils_CD4
|full_id=C675_Eosinophils_CD14_Natural_CD8_Neutrophils_Basophils_CD4
|gostat_on_coexpression_clusters=GO:0005618!cell wall!0.00541614540821025!8209$GO:0030312!external encapsulating structure!0.00812373980212789!8209$GO:0005739!mitochondrion!0.0132731077032574!10730;8209
|gostat_on_coexpression_clusters=GO:0005618!cell wall!0.00541614540821025!8209$GO:0030312!external encapsulating structure!0.00812373980212789!8209$GO:0005739!mitochondrion!0.0132731077032574!10730;8209

Revision as of 18:20, 12 September 2012


Full id: C675_Eosinophils_CD14_Natural_CD8_Neutrophils_Basophils_CD4



Phase1 CAGE Peaks

Hg19::chr10:27444086..27444105,-p4@YME1L1
Hg19::chr12:49412702..49412735,+p@chr12:49412702..49412735
+
Hg19::chr12:50064927..50064942,+p@chr12:50064927..50064942
+
Hg19::chr17:75954523..75954527,-p@chr17:75954523..75954527
-
Hg19::chr19:41304544..41304552,-p@chr19:41304544..41304552
-
Hg19::chr19:54372647..54372650,-p7@ENST00000455835
Hg19::chr1:174968433..174968454,-p4@BC038430
Hg19::chr21:45559862..45559873,-p1@AK127364
Hg19::chr2:135810397..135810416,+p@chr2:135810397..135810416
+
Hg19::chr6:138029264..138029275,-p@chr6:138029264..138029275
-
Hg19::chr7:130598148..130598162,-p2@LOC646329
Hg19::chr9:134609727..134609746,-p@chr9:134609727..134609746
-


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:0005618cell wall0.00541614540821025
GO:0030312external encapsulating structure0.00812373980212789
GO:0005739mitochondrion0.0132731077032574



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
leukocyte6.22e-52140
hematopoietic stem cell2.36e-50172
angioblastic mesenchymal cell2.36e-50172
hematopoietic cell2.45e-49182
hematopoietic oligopotent progenitor cell3.17e-46165
hematopoietic multipotent progenitor cell3.17e-46165
nongranular leukocyte8.51e-42119
hematopoietic lineage restricted progenitor cell2.71e-41124
CD14-positive, CD16-negative classical monocyte8.68e-2642
myeloid leukocyte6.64e-2576
classical monocyte2.39e-2445
myeloid cell3.59e-24112
common myeloid progenitor3.59e-24112
granulocyte monocyte progenitor cell1.12e-2171
lymphocyte1.23e-2053
common lymphoid progenitor1.23e-2053
lymphoid lineage restricted progenitor cell1.98e-2052
macrophage dendritic cell progenitor9.65e-2065
myeloid lineage restricted progenitor cell3.40e-1970
monopoietic cell9.11e-1963
monocyte9.11e-1963
monoblast9.11e-1963
promonocyte9.11e-1963
mesenchymal cell1.40e-16358
connective tissue cell8.92e-16365
motile cell2.30e-14390
stem cell3.03e-11444
multi fate stem cell9.12e-11430
lymphocyte of B lineage2.68e-1024
pro-B cell2.68e-1024
somatic stem cell2.71e-10436
native cell2.77e-10722
T cell1.69e-0925
pro-T cell1.69e-0925
mature alpha-beta T cell4.45e-0818
alpha-beta T cell4.45e-0818
immature T cell4.45e-0818
mature T cell4.45e-0818
immature alpha-beta T cell4.45e-0818
B cell1.70e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.05e-25102
blood island5.05e-25102
hemolymphoid system7.82e-23112
bone marrow9.25e-2180
bone element1.08e-2086
immune system3.74e-17115
skeletal element4.54e-15101
skeletal system4.54e-15101
connective tissue8.75e-15375


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#90563.168100788481320.006015621942674210.0269653435800228
E2F1#186972.862643708679610.004360763229147680.0206724048335961
E2F4#187444.222686771761480.01146510237446740.0419391204121398
E2F6#187672.926674176823480.003823084322472550.0188713065296678
EBF1#187964.45323342328450.001011881476986250.00717934032438631
EGR1#195872.909771138639250.003957340760479120.0189962178463795
ELF1#199782.838731972538360.001804270346094040.0109149786072588
ETS1#211364.864380461101170.0006281377526434450.00516958855384782
GTF2B#295937.985957483581060.005455491186982880.02471655579027
GTF2F1#296244.246553625585880.01124277021557680.0412761865414498
HEY1#2346272.356731441811660.01346982061264720.0475776039963561
HMGN3#932453.407728218062750.01028040559075030.0381941332393856
IRF1#365974.455012189578940.0002850277586319370.00303105733466662
MAX#414963.226277754503560.00548348112691290.0248325941121176
MYC#460973.046331091772150.003007674913179810.0159816107991649
NFKB1#479083.658708949462560.0002973737521670860.0031041896354401
PAX5#507963.334782765588910.004629821511058920.021860569139359
POLR2A#5430111.968498745178230.00153515886455670.00975958465153622
POU2F2#545275.311905700349819.21465586752959e-050.00134202962508565
SIN3A#2594273.155182757308830.002433775882281460.0137069197244173
SP1#666773.324055803915520.001772697031948130.0108879502069884
SPI1#668853.418468128551140.01014461279531980.0378958872498179
SRF#672244.59905942072260.008506629938930720.0324668880350821
WRNIP1#56897218.30332739156270.005147580523620290.0239287916636124



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.