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Coexpression cluster:C500

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Full id: C500_Neutrophils_Monocytederived_blood_CD14_Eosinophils_lung_mixed



Phase1 CAGE Peaks

  Short description
Hg19::chr12:65090856..65090873,+ p@chr12:65090856..65090873
+
Hg19::chr15:45007619..45007649,+ p6@B2M
Hg19::chr15:45007659..45007713,+ p3@B2M
Hg19::chr15:45007740..45007774,+ p5@B2M
Hg19::chr15:45007776..45007836,+ p2@B2M
Hg19::chr15:45009798..45009900,+ p@chr15:45009798..45009900
+
Hg19::chr15:45009902..45010022,+ p@chr15:45009902..45010022
+
Hg19::chr1:203276836..203276855,+ p@chr1:203276836..203276855
+
Hg19::chr6:29691484..29691495,+ p3@HLA-F
Hg19::chr6:30458007..30458044,+ p@chr6:30458007..30458044
+
Hg19::chr6:30458081..30458117,+ p@chr6:30458081..30458117
+
Hg19::chr6:30458196..30458253,+ p@chr6:30458196..30458253
+
Hg19::chr6:30460680..30460737,+ +
p@chr6:30460680..30460737
Hg19::chr6:31239406..31239455,+ p@chr6:31239406..31239455
+
Hg19::chr6:31321862..31321941,- p1@X07061
p1@X07062
Hg19::chr6:31322867..31322902,+ p@chr6:31322867..31322902
+
Hg19::chr6:31322916..31322974,- p4@HLA-B
Hg19::chr6:31323216..31323285,- p3@HLA-C
p5@HLA-B
Hg19::chr6:31324641..31324664,- p10@HLA-B


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


p.valueFDRnGenesnPathwayName
0.0001517463875231860.008004621941848052204Endocytosis (KEGG):04144
8.87028067484744e-050.005104443333798572156Phagosome (KEGG):04145
6.73840783266509e-050.0042654121580772136Cell adhesion molecules (CAMs) (KEGG):04514
1.96249599285332e-086.21129981738076e-06378Antigen processing and presentation (KEGG):04612
7.28240379719336e-060.000768293600603899245Type I diabetes mellitus (KEGG):04940
1.05241687813521e-050.000951685548370838254Autoimmune thyroid disease (KEGG):05320
5.45153351157612e-060.000768293600603899239Allograft rejection (KEGG):05330
6.64274556874299e-060.000768293600603899243Graft-versus-host disease (KEGG):05332
1.87899740683929e-050.00132156150947697272Viral myocarditis (KEGG):05416
1.48230348787841e-050.00117287263478379264Proteasome Degradation (Wikipathways):WP183
5.70320151504265e-060.0007682936006038993511Signaling in Immune system (Reactome):REACT_6900
5.37212511845661e-093.40055519998304e-06351{HLA-A,53} (Static Module):NA



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


GO IDGO nameFDR corrected p-value
GO:0002474antigen processing and presentation of peptide antigen via MHC class I3.44283425591547e-07
GO:0048002antigen processing and presentation of peptide antigen3.44283425591547e-07
GO:0042612MHC class I protein complex2.48279173867282e-06
GO:0042611MHC protein complex7.44220434057843e-06
GO:0019882antigen processing and presentation8.68789839607204e-06
GO:0032393MHC class I receptor activity1.03087902489797e-05
GO:0006955immune response0.000146634857782203
GO:0002376immune system process0.000203303733848579
GO:0044459plasma membrane part0.000810460688395914
GO:0043234protein complex0.00146544028199587
GO:0005886plasma membrane0.0029844998842909
GO:0032991macromolecular complex0.0029844998842909
GO:0004888transmembrane receptor activity0.0188521394295296
GO:0044425membrane part0.0201582891042318
GO:0004872receptor activity0.0354197492238477
GO:0016020membrane0.0354197492238477
GO:0004871signal transducer activity0.0442459626345693
GO:0060089molecular transducer activity0.0442459626345693



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


Cell Type
Ontology termp-valuen
leukocyte2.70e-44140
nongranular leukocyte4.23e-39119
hematopoietic lineage restricted progenitor cell8.37e-35124
hematopoietic stem cell3.27e-31172
angioblastic mesenchymal cell3.27e-31172
hematopoietic cell4.99e-30182
hematopoietic oligopotent progenitor cell7.79e-30165
hematopoietic multipotent progenitor cell7.79e-30165
myeloid leukocyte2.28e-2776
CD14-positive, CD16-negative classical monocyte1.05e-2542
macrophage dendritic cell progenitor1.17e-2565
monopoietic cell4.83e-2563
monocyte4.83e-2563
monoblast4.83e-2563
promonocyte4.83e-2563
classical monocyte2.58e-2345
granulocyte monocyte progenitor cell1.34e-2271
myeloid lineage restricted progenitor cell4.75e-2170
myeloid cell1.37e-16112
common myeloid progenitor1.37e-16112
mesenchymal cell4.16e-15358
connective tissue cell2.56e-14365
lymphocyte8.38e-1353
common lymphoid progenitor8.38e-1353
lymphoid lineage restricted progenitor cell9.46e-1352
multi fate stem cell1.43e-12430
somatic stem cell4.09e-11436
stem cell2.24e-10444
mature alpha-beta T cell3.33e-0918
alpha-beta T cell3.33e-0918
immature T cell3.33e-0918
mature T cell3.33e-0918
immature alpha-beta T cell3.33e-0918
motile cell3.52e-09390
T cell7.55e-0825
pro-T cell7.55e-0825
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.84e-28112
hematopoietic system5.08e-28102
blood island5.08e-28102
bone marrow8.48e-2180
immune system7.82e-18115
bone element1.29e-1786
connective tissue2.80e-14375
skeletal element2.25e-13101
skeletal system2.25e-13101
lateral plate mesoderm3.33e-12216
musculoskeletal system3.70e-09167
blood6.79e-0815
haemolymphatic fluid6.79e-0815
organism substance6.79e-0815


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
CTCF#10664102.821187564776330.000897037362883790.00667562242712128
POLR2A#5430182.034429325160281.12471092130166e-050.000287760127167623
RFX5#599363.804603419114240.003431185083611320.0174608750644293
WRNIP1#56897211.55999624730270.01278646128291030.0460103786495957



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.