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Coexpression cluster:C2218

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Full id: C2218_Mast_splenic_CD8_thymus_CD4_Hodgkin_Natural



Phase1 CAGE Peaks

  Short description
Hg19::chr12:55378625..55378672,+ p@chr12:55378625..55378672
+
Hg19::chr22:40297105..40297116,+ p7@GRAP2
Hg19::chr22:40297138..40297143,+ p8@GRAP2
Hg19::chr22:40297150..40297195,+ p1@GRAP2


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
hematopoietic stem cell4.27e-48168
angioblastic mesenchymal cell4.27e-48168
hematopoietic oligopotent progenitor cell2.14e-45161
hematopoietic multipotent progenitor cell2.14e-45161
leukocyte3.58e-45136
hematopoietic cell4.42e-44177
nucleate cell1.02e-4355
lymphocyte8.31e-4253
common lymphoid progenitor8.31e-4253
lymphoid lineage restricted progenitor cell7.17e-4152
hematopoietic lineage restricted progenitor cell5.46e-39120
nongranular leukocyte1.70e-36115
mature alpha-beta T cell1.47e-2418
alpha-beta T cell1.47e-2418
immature T cell1.47e-2418
mature T cell1.47e-2418
immature alpha-beta T cell1.47e-2418
T cell4.07e-2225
pro-T cell4.07e-2225
lymphocyte of B lineage4.16e-1624
pro-B cell4.16e-1624
CD8-positive, alpha-beta T cell4.70e-1611
B cell2.24e-1214
myeloid cell3.89e-12108
common myeloid progenitor3.89e-12108
CD4-positive, alpha-beta T cell3.24e-096
mesenchymal cell1.01e-08354
histamine secreting cell1.04e-085
biogenic amine secreting cell1.04e-085
granulocytopoietic cell1.04e-085
mast cell1.04e-085
mast cell progenitor1.04e-085
basophil mast progenitor cell1.04e-085
myeloid leukocyte1.13e-0872
connective tissue cell4.12e-08361
myeloid lineage restricted progenitor cell1.20e-0766
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.21e-1498
blood island9.21e-1498
hemolymphoid system6.56e-13108
hemopoietic organ1.40e-097
immune organ1.40e-097
blood2.38e-0915
haemolymphatic fluid2.38e-0915
organism substance2.38e-0915
connective tissue1.26e-07371
immune system1.59e-0793
adult organism1.77e-07114
Disease
Ontology termp-valuen
chronic leukemia9.72e-098


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCL11A#53335428.36945510360711.542446414682e-065.88354861588654e-05
EBF1#187936.679850134926750.005184294118278910.0240374025935153
ELF1#199744.258097958807540.003041525565781240.0160634077655943
IRF4#3662421.91451268674414.33289161192893e-060.00013609710287466
MEF2A#4205418.74323090964418.0978922767748e-060.000224273606866636
NFKB1#479045.488063424193840.001102199566301980.00766906199233926
PAX5#507946.669565531177830.0005052774169483260.00443301983775758
POU2F2#545249.106124057742520.000145395665174930.00188165772926945
SP1#666745.69838137814090.0009482606065333980.00683238285517361
SPI1#668848.204323508522730.000220661881527680.00249196650571684
SRF#6722310.34788369662590.001439893778401260.0092360315884074
TAF1#687243.343046285745290.008005664898701650.0321442326844605
TBP#690843.706770687096390.005296377814784350.0243624048710972



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.