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Coexpression cluster:C1387

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Full id: C1387_Neutrophils_Eosinophils_Whole_brain_parietal_optic_temporal



Phase1 CAGE Peaks

Hg19::chr14:102829269..102829295,+p2@TECPR2
Hg19::chr14:102829302..102829332,+p3@TECPR2
Hg19::chr19:17858547..17858582,+p1@FCHO1
Hg19::chr19:18220958..18221027,+p@chr19:18220958..18221027
+
Hg19::chr19:4969116..4969131,+p1@KDM4B
Hg19::chr3:113557654..113557682,+p3@GRAMD1C


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
leukocyte1.51e-25140
nongranular leukocyte2.42e-20119
CD14-positive, CD16-negative classical monocyte1.12e-1942
hematopoietic lineage restricted progenitor cell1.05e-18124
hematopoietic stem cell4.80e-17172
angioblastic mesenchymal cell4.80e-17172
myeloid leukocyte5.04e-1776
hematopoietic cell1.27e-16182
classical monocyte1.71e-1645
hematopoietic oligopotent progenitor cell1.02e-15165
hematopoietic multipotent progenitor cell1.02e-15165
granulocyte monocyte progenitor cell8.73e-1471
monopoietic cell2.33e-1363
monocyte2.33e-1363
monoblast2.33e-1363
promonocyte2.33e-1363
macrophage dendritic cell progenitor2.40e-1365
myeloid lineage restricted progenitor cell1.50e-1270
myeloid cell2.00e-09112
common myeloid progenitor2.00e-09112
lymphoid lineage restricted progenitor cell8.17e-0752
lymphocyte8.42e-0753
common lymphoid progenitor8.42e-0753
Uber Anatomy
Ontology termp-valuen
adult organism7.70e-30115
neural tube2.32e-2757
neural rod2.32e-2757
future spinal cord2.32e-2757
neural keel2.32e-2757
central nervous system1.89e-2482
regional part of brain1.67e-2359
regional part of forebrain3.53e-2141
forebrain3.53e-2141
future forebrain3.53e-2141
regional part of nervous system4.91e-2194
nervous system4.91e-2194
anterior neural tube7.54e-2142
brain1.17e-2069
future brain1.17e-2069
neural plate2.01e-1986
presumptive neural plate2.01e-1986
neurectoderm4.62e-1990
telencephalon2.80e-1834
gray matter2.89e-1834
brain grey matter2.89e-1834
regional part of telencephalon1.06e-1733
cerebral hemisphere5.00e-1732
hematopoietic system5.33e-17102
blood island5.33e-17102
hemolymphoid system2.90e-16112
pre-chordal neural plate1.15e-1561
regional part of cerebral cortex2.39e-1422
neocortex4.07e-1320
cerebral cortex4.89e-1325
pallium4.89e-1325
bone marrow1.21e-1080
immune system7.15e-10115
bone element7.31e-1086
anterior region of body5.27e-08129
craniocervical region5.27e-08129
posterior neural tube1.14e-0715
chordal neural plate1.14e-0715
head7.04e-07123
lateral plate mesoderm7.55e-07216
nucleus of brain9.17e-079
neural nucleus9.17e-079


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#90566.336201576962631.54467812014647e-050.000362445828330661
EGR1#195854.156815912341780.001617966818864440.0101324480779147
ELF1#199753.548414965672950.003446837775721690.017528572355193
IRF1#365945.091442502375930.003535240765893810.0179440615449642
IRF3#3661215.66065073716320.006417620989932530.0279142858926144
MEF2A#420539.371615454822030.002687399947103910.0148008945354419
NFKB1#479043.658708949462560.01207927289015230.0438265479025401
PBX3#5090310.95725634337210.001711753441810940.0106883784353278
POLR2A#543062.147453176558070.01019570676818780.0380133306855193
SP1#666743.79892091876060.01052246616798510.0389438266458128
SP2#6668417.43568699589643.01067847232342e-050.000619570933932978
SREBF1#6720323.50292472024410.0001833718571432050.00222042590007874
TFAP2A#702038.259317186522480.003860738477055590.0190436719314792
TFAP2C#702247.206152406573480.0009421413689212550.00681839806172594
ZNF143#770236.750438276113950.006850259204468580.0290390153450296



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.