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Coexpression cluster:C4003

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Full id: C4003_CD14_CD4_immature_CD8_Natural_Neutrophils_CD19



Phase1 CAGE Peaks

Hg19::chr1:89357240..89357257,-p1@GTF2B
Hg19::chr3:93781920..93781933,+p2@NSUN3
Hg19::chr5:42992418..42992435,+p@chr5:42992418..42992435
+


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
hematopoietic stem cell2.22e-59172
angioblastic mesenchymal cell2.22e-59172
leukocyte1.27e-55140
hematopoietic oligopotent progenitor cell1.81e-55165
hematopoietic multipotent progenitor cell1.81e-55165
hematopoietic cell8.36e-54182
hematopoietic lineage restricted progenitor cell4.99e-49124
nongranular leukocyte6.60e-47119
myeloid cell7.97e-31112
common myeloid progenitor7.97e-31112
myeloid leukocyte1.35e-2776
granulocyte monocyte progenitor cell3.98e-2571
myeloid lineage restricted progenitor cell5.22e-2570
CD14-positive, CD16-negative classical monocyte5.75e-2442
classical monocyte4.32e-2345
macrophage dendritic cell progenitor6.87e-2365
lymphocyte4.29e-2253
common lymphoid progenitor4.29e-2253
monopoietic cell4.56e-2263
monocyte4.56e-2263
monoblast4.56e-2263
promonocyte4.56e-2263
lymphoid lineage restricted progenitor cell9.58e-2252
mesenchymal cell1.24e-16358
connective tissue cell1.78e-15365
motile cell4.98e-12390
T cell1.03e-1125
pro-T cell1.03e-1125
mature alpha-beta T cell3.68e-1018
alpha-beta T cell3.68e-1018
immature T cell3.68e-1018
mature T cell3.68e-1018
immature alpha-beta T cell3.68e-1018
lymphocyte of B lineage1.26e-0924
pro-B cell1.26e-0924
B cell6.25e-0814
CD8-positive, alpha-beta T cell8.51e-0711
multi fate stem cell9.85e-07430
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.76e-32102
blood island5.76e-32102
hemolymphoid system3.90e-28112
bone marrow5.16e-2380
bone element6.30e-2386
skeletal element8.27e-17101
skeletal system8.27e-17101
immune system2.35e-15115
connective tissue7.12e-15375
blood3.43e-0815
haemolymphatic fluid3.43e-0815
organism substance3.43e-0815
Disease
Ontology termp-valuen
hematologic cancer9.18e-0751
immune system cancer9.18e-0751


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
BRCA1#672213.45615376214920.007119807716084560.0296272849653421
E2F6#187635.017155731697390.00791769806886330.0322686517058462
EGR1#195834.988179094810140.008056488137383440.032105142116155
ELF1#199734.258097958807540.01295179875054610.0462879550254349
ELK4#2005210.8237877723120.01091284719516480.0401991693078377
GABPB1#255337.067683836182170.002832212825417420.0154284099349974
MEF2A#4205212.4954872730960.008235029478029740.0324869020040775
MYC#460935.22228187160940.007020843755740150.0294880519989442
NFKB1#479035.488063424193840.006049381815655430.0269834879749397
PAX5#507936.669565531177830.003370290999677260.0173078537500759
POU2F2#545239.106124057742520.001324165192682130.00882993797462195
SIN3A#2594235.408884726815140.006318961977991520.0277148525961472
SPI1#668838.204323508522730.001810593189410520.0109159234606503
STAT1#6772213.80439166479950.006770931708444080.0287540900540069
TRIM28#10155212.39368336350830.008368344129438470.032917083821115
ZEB1#6935316.88843201754390.0002075486917327580.00242979237931594



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.