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Coexpression cluster:C1354

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Full id: C1354_CD4_CD19_CD8_cord_Natural_Mast_thymus



Phase1 CAGE Peaks

Hg19::chr11:94227129..94227182,+p1@ANKRD49
Hg19::chr19:21203451..21203475,+p1@ZNF430
Hg19::chr19:21324829..21324855,+p1@ZNF431
Hg19::chr4:56814968..56815018,+p1@CEP135
Hg19::chr4:84376953..84377040,-p1@HELQ
Hg19::chr7:86781734..86781777,+p1@DMTF1


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


GO IDGO nameFDR corrected p-value
GO:0006355regulation of transcription, DNA-dependent0.0283845759598042
GO:0006351transcription, DNA-dependent0.0283845759598042
GO:0032774RNA biosynthetic process0.0283845759598042
GO:0003677DNA binding0.0283845759598042
GO:0045449regulation of transcription0.0283845759598042
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0283845759598042
GO:0006350transcription0.0283845759598042
GO:0010468regulation of gene expression0.0283845759598042
GO:0031323regulation of cellular metabolic process0.0283845759598042
GO:0019222regulation of metabolic process0.0283845759598042
GO:0016070RNA metabolic process0.0283845759598042
GO:0043229intracellular organelle0.0364791675777369
GO:0043226organelle0.0364791675777369
GO:0010467gene expression0.0463822808005125
GO:0005813centrosome0.0463822808005125
GO:0050794regulation of cellular process0.0463822808005125
GO:0005815microtubule organizing center0.0463822808005125
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0463822808005125
GO:0005634nucleus0.0473610801434053
GO:0050789regulation of biological process0.0473610801434053
GO:0044424intracellular part0.0473610801434053
GO:0003676nucleic acid binding0.0485494265355204



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
hematopoietic stem cell8.05e-55172
angioblastic mesenchymal cell8.05e-55172
hematopoietic oligopotent progenitor cell1.39e-50165
hematopoietic multipotent progenitor cell1.39e-50165
hematopoietic cell4.13e-50182
leukocyte6.49e-49140
hematopoietic lineage restricted progenitor cell1.55e-40124
nongranular leukocyte3.54e-38119
myeloid cell1.25e-27112
common myeloid progenitor1.25e-27112
myeloid leukocyte4.36e-2176
lymphocyte6.61e-2153
common lymphoid progenitor6.61e-2153
lymphoid lineage restricted progenitor cell9.54e-2152
granulocyte monocyte progenitor cell8.62e-1971
myeloid lineage restricted progenitor cell2.56e-1870
CD14-positive, CD16-negative classical monocyte3.49e-1742
macrophage dendritic cell progenitor1.72e-1665
classical monocyte6.83e-1645
monopoietic cell1.36e-1563
monocyte1.36e-1563
monoblast1.36e-1563
promonocyte1.36e-1563
mature alpha-beta T cell1.09e-1118
alpha-beta T cell1.09e-1118
immature T cell1.09e-1118
mature T cell1.09e-1118
immature alpha-beta T cell1.09e-1118
T cell1.77e-1025
pro-T cell1.77e-1025
lymphocyte of B lineage8.40e-1024
pro-B cell8.40e-1024
B cell1.43e-0814
CD8-positive, alpha-beta T cell3.53e-0811
mesenchymal cell1.68e-07358
motile cell8.64e-07390
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.98e-24102
blood island2.98e-24102
hemolymphoid system6.27e-21112
bone marrow1.95e-1580
bone element3.82e-1386
skeletal element2.75e-10101
skeletal system2.75e-10101
adult organism7.19e-10115
immune system2.20e-08115
blood4.84e-0815
haemolymphatic fluid4.84e-0815
organism substance4.84e-0815


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
CHD2#110658.620019028430714.6560374997265e-050.000814798760780724
E2F4#1874510.55671692940371.71705502564041e-050.000392573357755821
ELF1#199764.258097958807540.0001677224776288830.0020513839841999
ELK4#2005410.8237877723120.0001950599973010460.00234888401454214
GABPB1#255367.067683836182178.01905956107035e-060.000222799298084232
GTF2F1#296236.369830438378830.008068208196303160.0319143883579027
HEY1#2346264.040111043105710.0002298968555807510.00252951935313928
IRF1#365956.364303127969920.000205667514205090.00243865911853604
IRF3#3661323.49097610574480.0001836473514994550.0022235040277361
MAX#414944.301703672671410.006644923910676370.0282937544156527
MXI1#460146.64104775250620.001288516958039140.00863744689221113
NFKB1#479054.57338618682820.00102196259371130.00724348498979396
NFYA#480039.212790349915260.002822755564364270.0154486070526982
NFYB#4801411.17319550235760.0001723343348218770.00209918656338489
PAX5#507944.446377020785220.005874733519240790.0263586928734798
POLR2A#543062.147453176558070.01019570676818780.0380024774861801
RFX5#5993510.03992568932922.19894173045095e-050.000482570446284023
SIN3A#2594265.408884726815143.99207083571449e-050.000742392959421627
SP1#666743.79892091876060.01052246616798510.0389410667275501
SP2#6668313.07676524692230.001024340397937320.00725886055232567
SPI1#668845.469549005681820.00269730053614140.0148413345289538
TAF1#687263.343046285745290.0007162474284635620.00572729233453074
TAF7#687959.52755783743662.84599232912077e-050.000599742923448435
TBP#690863.706770687096390.000385416472907960.00377532461208352
TCF12#693858.862054085155354.06365504449859e-050.000743264569513815
TCF7L2#693458.975147135947793.818060286338e-050.000719773282030424
ZBTB33#10009210.55490834332710.01374250737140590.048380426325162
ZEB1#693538.444216008771930.003623843810733590.0183349783814168



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.