Coexpression cluster:C2138

Full id: C2138_Smooth_CD14_mesothelioma_Hair_meningioma_normal_mesenchymal

Phase1 CAGE Peaks

Hg19::chr11:57335090..57335155,-	p1@UBE2L6
Hg19::chr15:74287118..74287142,+	p2@PML
Hg19::chr17:41158760..41158822,+	p1@IFI35
Hg19::chr17:41158825..41158847,+	p2@IFI35

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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p.value	FDR	nGenes	nPathway	Name
7.03959989046011e-05	0.0222803336533063	2	139	Ubiquitin mediated proteolysis (KEGG):04120
5.70320151504265e-06	0.00361012655902199	3	511	Signaling in Immune system (Reactome):REACT_6900

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:0031571	G1 DNA damage checkpoint	0.0286350242431562
GO:0006977	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	0.0286350242431562
GO:0042771	DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis	0.0286350242431562
GO:0031575	G1/S transition checkpoint	0.0286350242431562
GO:0016605	PML body	0.0286350242431562
GO:0030330	DNA damage response, signal transduction by p53 class mediator	0.0286350242431562
GO:0016525	negative regulation of angiogenesis	0.0286350242431562
GO:0008630	DNA damage response, signal transduction resulting in induction of apoptosis	0.0286350242431562
GO:0005626	insoluble fraction	0.0286350242431562
GO:0000077	DNA damage checkpoint	0.0300596940472044
GO:0007093	mitotic cell cycle checkpoint	0.0300596940472044
GO:0031570	DNA integrity checkpoint	0.0300596940472044
GO:0008629	induction of apoptosis by intracellular signals	0.0349571040718196
GO:0045765	regulation of angiogenesis	0.0349571040718196
GO:0042770	DNA damage response, signal transduction	0.0369141724117895
GO:0001666	response to hypoxia	0.0379388436354144
GO:0030308	negative regulation of cell growth	0.0379388436354144
GO:0045792	negative regulation of cell size	0.0379388436354144
GO:0000075	cell cycle checkpoint	0.0379388436354144
GO:0045926	negative regulation of growth	0.0392541470303728
GO:0007088	regulation of mitosis	0.0410548490495792

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
nongranular leukocyte	3.52e-18	115
leukocyte	4.20e-18	136
myeloid leukocyte	3.54e-17	72
monopoietic cell	3.51e-16	59
monocyte	3.51e-16	59
monoblast	3.51e-16	59
promonocyte	3.51e-16	59
defensive cell	4.82e-16	48
phagocyte	4.82e-16	48
hematopoietic lineage restricted progenitor cell	8.84e-16	120
classical monocyte	7.66e-15	42
CD14-positive, CD16-negative classical monocyte	7.66e-15	42
macrophage dendritic cell progenitor	1.24e-14	61
myeloid lineage restricted progenitor cell	1.64e-14	66
connective tissue cell	2.38e-13	361
granulocyte monocyte progenitor cell	4.44e-13	67
hematopoietic stem cell	1.40e-12	168
angioblastic mesenchymal cell	1.40e-12	168
hematopoietic cell	2.42e-12	177
mesenchymal cell	4.26e-12	354
hematopoietic oligopotent progenitor cell	5.05e-12	161
hematopoietic multipotent progenitor cell	5.05e-12	161
multi fate stem cell	5.56e-12	427
somatic stem cell	1.06e-10	433
stem cell	3.99e-10	441
motile cell	1.94e-09	386
myeloid cell	1.37e-08	108
common myeloid progenitor	1.37e-08	108

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	2.07e-19	108
immune system	1.37e-17	93
hematopoietic system	5.18e-17	98
blood island	5.18e-17	98
bone marrow	3.04e-13	76
connective tissue	4.98e-13	371
skeletal element	5.26e-11	90
bone element	1.04e-10	82
skeletal system	5.94e-10	100
musculoskeletal system	5.05e-09	167
lateral plate mesoderm	2.37e-08	203
mesoderm	9.34e-07	315
mesoderm-derived structure	9.34e-07	315
presumptive mesoderm	9.34e-07	315

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
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101266922464243
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319839096667028
IRF4#3662	2	10.9572563433721	0.0117453018068803	0.0428111393365014
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186199270898034
RAD21#5885	3	7.76627542159225	0.003341119385872	0.0172615962177139
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.0079428877412123
SPI1#6688	3	6.15324263139204	0.00658038711305903	0.0280888155352423
STAT1#6772	3	15.5299406228994	0.00043408865517555	0.00404783795159636
STAT2#6773	3	48.9478283898305	1.42094046481278e-05	0.000340136606015544
STAT3#6774	3	7.88959874786568	0.00319076048168013	0.016738991056168
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0482715884091698
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342236433282897
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.0097600713442927
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00248125831543171

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.