Coexpression cluster:C3377

Full id: C3377_CD14_CD4_acute_immature_esophagus_NK_CD14CD16

Phase1 CAGE Peaks

Hg19::chr13:48987196..48987207,-	p3@LPAR6
Hg19::chr13:48987228..48987239,-	p2@LPAR6
Hg19::chr13:48987241..48987260,-	p1@LPAR6

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

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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

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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>

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Cell Type

Ontology term	p-value	n
defensive cell	5.01e-24	48
phagocyte	5.01e-24	48
macrophage dendritic cell progenitor	1.66e-21	61
classical monocyte	1.53e-20	42
CD14-positive, CD16-negative classical monocyte	1.53e-20	42
monopoietic cell	1.60e-20	59
monocyte	1.60e-20	59
monoblast	1.60e-20	59
promonocyte	1.60e-20	59
granulocyte monocyte progenitor cell	5.02e-18	67
myeloid lineage restricted progenitor cell	2.51e-16	66
myeloid leukocyte	4.97e-16	72
nongranular leukocyte	9.96e-16	115
stuff accumulating cell	2.20e-14	87
leukocyte	3.28e-14	136
hematopoietic lineage restricted progenitor cell	1.06e-13	120
mature alpha-beta T cell	1.25e-09	18
alpha-beta T cell	1.25e-09	18
immature T cell	1.25e-09	18
mature T cell	1.25e-09	18
immature alpha-beta T cell	1.25e-09	18
myeloid cell	2.78e-09	108
common myeloid progenitor	2.78e-09	108
hematopoietic stem cell	5.27e-09	168
angioblastic mesenchymal cell	5.27e-09	168
hematopoietic oligopotent progenitor cell	1.27e-08	161
hematopoietic multipotent progenitor cell	1.27e-08	161
hematopoietic cell	1.85e-07	177

Uber Anatomy

Ontology term	p-value	n
adult organism	4.14e-21	114
hemolymphoid system	5.90e-21	108
hematopoietic system	3.40e-20	98
blood island	3.40e-20	98
immune system	2.81e-17	93
bone marrow	4.38e-15	76
bone element	1.65e-12	82
skeletal element	1.22e-11	90
skeletal system	1.00e-10	100
lateral plate mesoderm	4.69e-07	203

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

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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

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

TF	#promoters	Enrichment	p-value	q-value
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460845226801677
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167123206760354
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00580111175073279
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107093815128724
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00436362180039532
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000849805383947738
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00390339362613672
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00443562758061199
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245844169797498
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0108920305344649
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00641801418882482
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00612384974447526

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

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This analysis result is provided for C0 - C305 clusters.