Coexpression cluster:C3023

Full id: C3023_Whole_CD14_Reticulocytes_Neutrophils_blood_Eosinophils_immature

Phase1 CAGE Peaks

Hg19::chr10:51572408..51572454,+	p3@NCOA4
Hg19::chr13:27745913..27745924,-	p2@USP12
Hg19::chr13:27745936..27745961,-	p1@USP12

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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GO ID	GO name	FDR corrected p-value
GO:0008584	male gonad development	0.0257906972704573
GO:0050681	androgen receptor binding	0.0257906972704573
GO:0046546	development of primary male sexual characteristics	0.0257906972704573
GO:0035258	steroid hormone receptor binding	0.0257906972704573
GO:0046661	male sex differentiation	0.0257906972704573
GO:0030521	androgen receptor signaling pathway	0.0257906972704573
GO:0030518	steroid hormone receptor signaling pathway	0.0257906972704573
GO:0008406	gonad development	0.0257906972704573
GO:0048608	reproductive structure development	0.0257906972704573
GO:0030522	intracellular receptor-mediated signaling pathway	0.0257906972704573
GO:0035257	nuclear hormone receptor binding	0.0257906972704573
GO:0051427	hormone receptor binding	0.0257906972704573
GO:0045137	development of primary sexual characteristics	0.0257906972704573
GO:0007548	sex differentiation	0.0323204795991889
GO:0003006	reproductive developmental process	0.0323974185904191
GO:0004221	ubiquitin thiolesterase activity	0.0431014388996514
GO:0004843	ubiquitin-specific protease activity	0.0431014388996514
GO:0019783	small conjugating protein-specific protease activity	0.0431014388996514

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
myeloid leukocyte	1.12e-30	72
granulocyte monocyte progenitor cell	2.23e-28	67
myeloid lineage restricted progenitor cell	6.80e-28	66
myeloid cell	3.82e-26	108
common myeloid progenitor	3.82e-26	108
macrophage dendritic cell progenitor	1.39e-25	61
defensive cell	8.76e-25	48
phagocyte	8.76e-25	48
monopoietic cell	2.51e-24	59
monocyte	2.51e-24	59
monoblast	2.51e-24	59
promonocyte	2.51e-24	59
leukocyte	5.15e-23	136
classical monocyte	6.26e-23	42
CD14-positive, CD16-negative classical monocyte	6.26e-23	42
hematopoietic stem cell	2.03e-20	168
angioblastic mesenchymal cell	2.03e-20	168
hematopoietic oligopotent progenitor cell	3.46e-19	161
hematopoietic multipotent progenitor cell	3.46e-19	161
hematopoietic lineage restricted progenitor cell	1.13e-18	120
hematopoietic cell	2.18e-18	177
nongranular leukocyte	1.44e-15	115
stuff accumulating cell	2.97e-10	87
mesenchymal cell	1.30e-08	354
connective tissue cell	4.04e-07	361

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.24e-30	98
blood island	1.24e-30	98
hemolymphoid system	8.71e-28	108
bone marrow	1.86e-23	76
bone element	3.51e-22	82
immune system	1.72e-19	93
skeletal element	3.99e-18	90
skeletal system	2.46e-16	100
lateral plate mesoderm	1.12e-14	203
blood	1.64e-10	15
haemolymphatic fluid	1.64e-10	15
organism substance	1.64e-10	15
mesoderm	5.81e-10	315
mesoderm-derived structure	5.81e-10	315
presumptive mesoderm	5.81e-10	315
connective tissue	8.92e-07	371

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278183045681942
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323399520085029
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032023718868175
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00912379642705261
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0318933956705401
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0459842571970453
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293077221713796
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172206370702198
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00661599727084839
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245331215215874
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327787460753686
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139576824831113

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.