Coexpression cluster:C1055

Full id: C1055_CD19_thymus_CD4_CD8_Neutrophils_Natural_cerebellum

Phase1 CAGE Peaks

Hg19::chr17:8151353..8151381,-	p1@CTC1
Hg19::chr1:204485503..204485555,+	p1@MDM4
Hg19::chr2:206950781..206950947,-	p1@INO80D
Hg19::chr4:76439596..76439643,-	p2@RCHY1
Hg19::chr4:78741389..78741433,-	p@chr4:78741389..78741433 -
Hg19::chr5:56469653..56469722,+	p2@GPBP1
Hg19::chr7:21467642..21467671,+	p2@SP4
Hg19::chr7:21467674..21467727,+	p1@SP4

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:0045023	G0 to G1 transition	0.0105964942920282
GO:0000320	re-entry into mitotic cell cycle	0.0105964942920282
GO:0042177	negative regulation of protein catabolic process	0.0190677949582778
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0190677949582778
GO:0009895	negative regulation of catabolic process	0.0190677949582778
GO:0050821	protein stabilization	0.0233248915267865
GO:0042176	regulation of protein catabolic process	0.0233248915267865
GO:0006366	transcription from RNA polymerase II promoter	0.0233248915267865
GO:0031647	regulation of protein stability	0.0247044173842433
GO:0009894	regulation of catabolic process	0.026464343452305

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
leukocyte	6.80e-40	136
hematopoietic stem cell	8.80e-39	168
angioblastic mesenchymal cell	8.80e-39	168
hematopoietic oligopotent progenitor cell	2.03e-35	161
hematopoietic multipotent progenitor cell	2.03e-35	161
hematopoietic cell	1.02e-34	177
hematopoietic lineage restricted progenitor cell	5.15e-32	120
nongranular leukocyte	8.18e-31	115
nucleate cell	3.35e-22	55
lymphocyte	1.34e-21	53
common lymphoid progenitor	1.34e-21	53
lymphoid lineage restricted progenitor cell	1.87e-21	52
myeloid cell	6.16e-15	108
common myeloid progenitor	6.16e-15	108
myeloid leukocyte	4.64e-14	72
mature alpha-beta T cell	6.85e-12	18
alpha-beta T cell	6.85e-12	18
immature T cell	6.85e-12	18
mature T cell	6.85e-12	18
immature alpha-beta T cell	6.85e-12	18
classical monocyte	1.70e-11	42
CD14-positive, CD16-negative classical monocyte	1.70e-11	42
granulocyte monocyte progenitor cell	2.14e-11	67
myeloid lineage restricted progenitor cell	3.44e-11	66
T cell	5.90e-11	25
pro-T cell	5.90e-11	25
lymphocyte of B lineage	6.67e-10	24
pro-B cell	6.67e-10	24
macrophage dendritic cell progenitor	6.94e-10	61
defensive cell	1.45e-09	48
phagocyte	1.45e-09	48
monopoietic cell	2.82e-09	59
monocyte	2.82e-09	59
monoblast	2.82e-09	59
promonocyte	2.82e-09	59
B cell	2.61e-08	14
CD8-positive, alpha-beta T cell	3.16e-08	11

Uber Anatomy

Ontology term	p-value	n
adult organism	2.14e-30	114
hematopoietic system	1.29e-15	98
blood island	1.29e-15	98
neural tube	1.69e-14	56
neural rod	1.69e-14	56
future spinal cord	1.69e-14	56
neural keel	1.69e-14	56
hemolymphoid system	1.72e-14	108
regional part of nervous system	1.54e-13	53
regional part of brain	1.54e-13	53
regional part of forebrain	1.99e-12	41
forebrain	1.99e-12	41
anterior neural tube	1.99e-12	41
future forebrain	1.99e-12	41
nervous system	8.53e-12	89
central nervous system	1.03e-11	81
telencephalon	3.04e-10	34
brain grey matter	4.03e-10	34
gray matter	4.03e-10	34
brain	5.02e-10	68
future brain	5.02e-10	68
regional part of telencephalon	1.47e-09	32
cerebral hemisphere	1.94e-09	32
immune system	2.29e-09	93
bone marrow	4.49e-08	76
blood	5.53e-08	15
haemolymphatic fluid	5.53e-08	15
organism substance	5.53e-08	15
neurectoderm	8.78e-08	86
bone element	9.36e-08	82
regional part of cerebral cortex	9.65e-08	22
neocortex	2.20e-07	20
cerebral cortex	2.68e-07	25
pallium	2.68e-07	25
neural plate	2.68e-07	82
presumptive neural plate	2.68e-07	82

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
CCNT2#905	6	4.75215118272197	0.000323589541710397	0.0033109991326239
E2F1#1869	7	4.29396556301941	9.58670853279727e-05	0.00137060404169311
E2F6#1876	5	3.13572233231087	0.0102488050142096	0.0381513739263985
EGR1#1958	5	3.11761193425634	0.0105139099038836	0.0389218147047958
HEY1#23462	8	4.04011104310571	1.4081650274634e-05	0.000339099255944779
HMGN3#9324	5	5.11159232709412	0.00110951597588993	0.0077086707694231
IRF1#3659	4	3.81858187678195	0.0132613631682617	0.0469047516909403
NFKB1#4790	7	4.80205549616961	4.48248622098168e-05	0.00079387210180279
PAX5#5079	5	4.16847845698614	0.00284750870610728	0.0154376537456986
PBX3#5090	4	10.9572563433721	0.000261492197563197	0.00280159864806142
POLR2A#5430	8	2.14745317655807	0.00221072578897191	0.0127209912217321
POU2F2#5452	4	4.55306202887126	0.00706247384683113	0.0294603069892238
TAF1#6872	8	3.34304628574529	6.40776711117462e-05	0.0010435377971682
TAF7#6879	4	5.71653470246196	0.00306854155518016	0.0161766398203756
TBP#6908	6	2.78007801532229	0.00639018112126301	0.0278041963972665
YY1#7528	7	4.29727440612212	9.53674534900876e-05	0.00136458165160313
ZNF263#10127	4	4.11092081850534	0.0101999278231626	0.0379924484440702

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.