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Coexpression cluster:C2095

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Full id: C2095_Mast_Retinal_CD14_bile_lung_cervical_Gingival



Phase1 CAGE Peaks

Hg19::chr11:112034761..112034772,-p4@IL18
Hg19::chr11:112034780..112034795,-p3@IL18
Hg19::chr11:112034803..112034824,-p1@IL18
Hg19::chr11:112034831..112034848,-p2@IL18


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>disease_data<br>


Cell Type
Ontology termp-valuen
myeloid cell7.61e-24108
common myeloid progenitor7.61e-24108
granulocyte monocyte progenitor cell2.01e-2367
myeloid leukocyte1.67e-2272
myeloid lineage restricted progenitor cell2.72e-2266
macrophage dendritic cell progenitor3.26e-2161
monopoietic cell3.80e-2059
monocyte3.80e-2059
monoblast3.80e-2059
promonocyte3.80e-2059
defensive cell1.76e-1748
phagocyte1.76e-1748
classical monocyte3.63e-1442
CD14-positive, CD16-negative classical monocyte3.63e-1442
endo-epithelial cell4.35e-1342
epithelial cell6.09e-13253
stuff accumulating cell3.77e-0987
endodermal cell7.47e-0958
hematopoietic stem cell4.49e-08168
angioblastic mesenchymal cell4.49e-08168
mesothelial cell6.45e-0819
hematopoietic oligopotent progenitor cell1.39e-07161
hematopoietic multipotent progenitor cell1.39e-07161
hematopoietic cell2.08e-07177
Uber Anatomy
Ontology termp-valuen
bone marrow8.95e-1976
hematopoietic system3.87e-1798
blood island3.87e-1798
immune system1.28e-1593
organ1.38e-15503
hemolymphoid system3.91e-15108
skeletal element6.35e-1590
bone element9.25e-1582
skeletal system1.15e-10100
subdivision of digestive tract2.28e-09118
endoderm-derived structure3.00e-09160
endoderm3.00e-09160
presumptive endoderm3.00e-09160
digestive system2.05e-08145
digestive tract2.05e-08145
primitive gut2.05e-08145
respiratory tract5.08e-0854
larynx1.94e-079
respiratory primordium2.05e-0738
endoderm of foregut2.05e-0738
respiratory system2.14e-0774
adult organism2.17e-07114
foregut8.62e-0787
Disease
Ontology termp-valuen
carcinoma3.91e-10106
squamous cell carcinoma8.63e-0714


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
CEBPB#105147.971147625824820.0002476385788090830.00267512676171305
CTCF#1066445.360256373075030.001211145381643620.00815491022587056
ELF1#199744.258097958807540.003041525565781240.0160528546879233
GATA3#2625427.2365163572061.81561517799785e-066.74567888918239e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000716446125928145
HEY1#2346244.040111043105710.00375304636917980.0185492598433945
TAF1#687243.343046285745290.008005664898701650.032118301949735
TBP#690843.706770687096390.005296377814784350.0243452490030484



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.