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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1739_CD14_Mast_Natural_Eosinophils_immature_Melanocyte_CD14CD16
|full_id=C1739_CD14_Mast_Natural_Eosinophils_immature_Melanocyte_CD14CD16
|id=C1739
|id=C1739

Revision as of 14:20, 12 September 2012


Full id: C1739_CD14_Mast_Natural_Eosinophils_immature_Melanocyte_CD14CD16



Phase1 CAGE Peaks

Hg19::chr15:45879287..45879319,-p@chr15:45879287..45879319
-
Hg19::chr17:66243950..66243978,-p1@BC056237
Hg19::chr17:66244002..66244037,-p2@BC056237
Hg19::chr19:10514593..10514606,+p@chr19:10514593..10514606
+
Hg19::chr1:115053955..115053993,+p@chr1:115053955..115053993
+


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


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><br>


Cell Type
Ontology termp-valuen
leukocyte4.79e-48140
hematopoietic stem cell2.73e-41172
angioblastic mesenchymal cell2.73e-41172
hematopoietic cell3.67e-41182
hematopoietic oligopotent progenitor cell1.08e-37165
hematopoietic multipotent progenitor cell1.08e-37165
hematopoietic lineage restricted progenitor cell2.27e-36124
nongranular leukocyte8.84e-36119
myeloid leukocyte9.76e-2476
classical monocyte5.82e-2245
CD14-positive, CD16-negative classical monocyte7.02e-2242
granulocyte monocyte progenitor cell5.70e-2171
myeloid cell5.79e-20112
common myeloid progenitor5.79e-20112
macrophage dendritic cell progenitor6.44e-1865
myeloid lineage restricted progenitor cell8.82e-1870
lymphoid lineage restricted progenitor cell6.57e-1752
lymphocyte6.89e-1753
common lymphoid progenitor6.89e-1753
monopoietic cell8.83e-1763
monocyte8.83e-1763
monoblast8.83e-1763
promonocyte8.83e-1763
mature alpha-beta T cell2.19e-1018
alpha-beta T cell2.19e-1018
immature T cell2.19e-1018
mature T cell2.19e-1018
immature alpha-beta T cell2.19e-1018
T cell2.16e-0825
pro-T cell2.16e-0825
lymphocyte of B lineage4.50e-0824
pro-B cell4.50e-0824
intermediate monocyte2.04e-079
CD14-positive, CD16-positive monocyte2.04e-079
B cell2.10e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.78e-25102
blood island1.78e-25102
hemolymphoid system3.33e-21112
bone marrow8.38e-2080
bone element6.25e-1986
immune system1.38e-12115
skeletal element7.54e-12101
skeletal system7.54e-12101
neural tube4.12e-0757
neural rod4.12e-0757
future spinal cord4.12e-0757
neural keel4.12e-0757


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#90556.336201576962639.78880505817628e-050.00138998370016434
CEBPB#105146.376918100659850.001113944176677320.00765288882173412
CHD2#110648.275218267293490.0004028373567101730.00387723995000034
E2F6#187655.017155731697390.0003144978599297790.00322682404884627
EGR1#195843.990543275848110.0067800983001440.0287626096254413
HMGN3#932446.542838178680470.00100801277768350.00722007039904583
IRF1#365946.109731002851120.001315525264767990.00880831793352381
MAX#414945.16204440720570.002526309009485180.013997092129529
MXI1#460147.969257303007440.0004668546380070170.00429433076790689
MYC#460955.22228187160940.0002573944848850610.00276393405376423
NANOG#79923211.69791139240510.01091164951956080.0402188729194781
NFKB1#479055.488063424193840.0002008162847462320.00238954676570715
NRF1#489937.326167668626540.004839689817117540.0226884085110844
PAX5#507956.669565531177837.57493746384605e-050.00116977509062046
POU2F2#545247.284899246194020.0006631223288743860.00542502216084224
SIN3A#2594255.408884726815140.0002159522671657270.00247953373246717
SP1#666744.558705102512720.00407573565781680.0194821619463924
SREBF1#6720328.2035096642939.31681575395428e-050.00135483002022728
TBP#690853.706770687096390.001428755106721120.009184891948224
USF1#739145.089199421766370.00266867775360040.0147171842807198
ZBTB33#10009212.66589001199250.009357016059651590.0353392905020776
ZBTB7A#5134145.881527446300720.001524947561042230.00971358857817088
ZNF143#770238.100525931336740.003624870512090980.018329517353165



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.