Coexpression cluster:C1026

Full id: C1026_Fibroblast_mesothelioma_Chondrocyte_epidermoid_Reticulocytes_clear_myxofibrosarcoma

Phase1 CAGE Peaks

Hg19::chr13:60738003..60738103,-	p1@DIAPH3
Hg19::chr15:66797627..66797684,+	p1@ZWILCH
Hg19::chr15:69706643..69706710,+	p1@KIF23
Hg19::chr15:69706713..69706724,+	p4@KIF23
Hg19::chr15:69706740..69706754,+	p2@KIF23
Hg19::chr16:46655208..46655316,-	p1@SHCBP1
Hg19::chr5:137514834..137514865,+	p2@KIF20A
Hg19::chr7:36429461..36429486,+	p1@ANLN

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

---

p.value	FDR	nGenes	nPathway	Name
6.67157721853038e-06	0.00422310837932973	3	200	DNA Replication (Reactome):REACT_383
2.59719623007301e-05	0.00822012606818106	3	315	Cell Cycle, Mitotic (Reactome):REACT_152

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 ID	GO name	FDR corrected p-value
GO:0007010	cytoskeleton organization and biogenesis	0.000253758630431385
GO:0006996	organelle organization and biogenesis	0.00299768850949541
GO:0003777	microtubule motor activity	0.00364784772441998
GO:0000921	septin ring assembly	0.00364784772441998
GO:0000022	mitotic spindle elongation	0.00364784772441998
GO:0032185	septin cytoskeleton organization and biogenesis	0.00364784772441998
GO:0051231	spindle elongation	0.00364784772441998
GO:0031106	septin ring organization	0.00364784772441998
GO:0005826	contractile ring	0.00364784772441998
GO:0044430	cytoskeletal part	0.00364784772441998
GO:0007018	microtubule-based movement	0.00364784772441998
GO:0005875	microtubule associated complex	0.00364784772441998
GO:0030705	cytoskeleton-dependent intracellular transport	0.00398926605803164
GO:0032153	cell division site	0.00404014110159463
GO:0032155	cell division site part	0.00404014110159463
GO:0043232	intracellular non-membrane-bound organelle	0.00404014110159463
GO:0043228	non-membrane-bound organelle	0.00404014110159463
GO:0007067	mitosis	0.00404014110159463
GO:0000087	M phase of mitotic cell cycle	0.00404014110159463
GO:0051301	cell division	0.00404014110159463
GO:0016043	cellular component organization and biogenesis	0.00541511559004266
GO:0005874	microtubule	0.00541511559004266
GO:0000279	M phase	0.0054585510817247
GO:0007017	microtubule-based process	0.00547302045029384
GO:0005856	cytoskeleton	0.00547302045029384
GO:0000278	mitotic cell cycle	0.00547302045029384
GO:0022403	cell cycle phase	0.00673190003874274
GO:0007052	mitotic spindle organization and biogenesis	0.00734938574349256
GO:0007096	regulation of exit from mitosis	0.00810540212515731
GO:0010458	exit from mitosis	0.00810540212515731
GO:0003779	actin binding	0.00821972114767682
GO:0044446	intracellular organelle part	0.00857158797561516
GO:0044422	organelle part	0.00857158797561516
GO:0042169	SH2 domain binding	0.00986760624313977
GO:0015630	microtubule cytoskeleton	0.00986760624313977
GO:0007051	spindle organization and biogenesis	0.00986760624313977
GO:0008092	cytoskeletal protein binding	0.0128918198713952
GO:0022402	cell cycle process	0.013414253511694
GO:0005871	kinesin complex	0.013414253511694
GO:0000776	kinetochore	0.0144770113713652
GO:0017048	Rho GTPase binding	0.0145784508666697
GO:0000910	cytokinesis	0.0151185788309958
GO:0044448	cell cortex part	0.0195287248205947
GO:0007049	cell cycle	0.020608139162833
GO:0046907	intracellular transport	0.0231279426470676
GO:0043234	protein complex	0.0231279426470676
GO:0005938	cell cortex	0.025374928519782
GO:0007088	regulation of mitosis	0.0260052133793836
GO:0043623	cellular protein complex assembly	0.0262310674601063
GO:0000775	chromosome, pericentric region	0.0279232946214486
GO:0017016	Ras GTPase binding	0.0279232946214486
GO:0005819	spindle	0.0279232946214486
GO:0051649	establishment of cellular localization	0.0287133850572141
GO:0031267	small GTPase binding	0.0290343433953052
GO:0051641	cellular localization	0.0290343433953052
GO:0051020	GTPase binding	0.0321997196792408
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0332532401154693
GO:0019904	protein domain specific binding	0.0406149369245473
GO:0032991	macromolecular complex	0.0410585754456491

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>disease_data<br>

---

Cell Type

Ontology term	p-value	n
animal cell	1.86e-23	679
eukaryotic cell	1.86e-23	679
epithelial cell	3.08e-19	254
non-terminally differentiated cell	1.79e-13	180
native cell	2.51e-13	722
embryonic cell	2.03e-11	248
squamous epithelial cell	4.97e-08	62
fibroblast	9.11e-08	75

Uber Anatomy

Ontology term	p-value	n
larynx	4.14e-07	9

Disease

Ontology term	p-value	n
cancer	1.63e-48	235
disease of cellular proliferation	7.74e-48	239
cell type cancer	6.52e-27	143
carcinoma	8.53e-21	106
organ system cancer	2.56e-19	137
hematologic cancer	4.29e-10	51
immune system cancer	4.29e-10	51
leukemia	2.78e-07	39
disease of anatomical entity	7.16e-07	39

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	#promoters	Enrichment	p-value	q-value
BRCA1#672	5	12.6151441520149	1.47177326411908e-05	0.000349421522917327
CEBPB#1051	5	4.98196726614051	0.00125052377879302	0.0084059633734546
CHD2#1106	6	7.75801712558764	1.92157406469162e-05	0.000434294035365349
E2F1#1869	8	4.90738921487932	2.97124777369457e-06	0.000101476176009446
E2F4#1874	8	12.6680603152844	1.5050509647149e-09	1.33434650003277e-07
E2F6#1876	7	4.39001126523521	8.25033297218753e-05	0.00123997197479104
ELF1#1997	7	3.7258357139566	0.000250341272551272	0.00269846136484491
ELK4#2005	5	10.1473010365425	4.23608403932528e-05	0.000758334557735847
ETS1#2113	7	8.51266580692704	8.8174082362229e-07	3.82267039760433e-05
FOS#2353	6	6.7484664816708	4.31702653902356e-05	0.000770052834686731
GABPB1#2553	6	5.30076287713663	0.00017345294309267	0.00211133472303676
HEY1#23462	8	4.04011104310571	1.4081650274634e-05	0.00033902108645286
IRF1#3659	7	6.68251828436841	4.6709523292352e-06	0.000145057862121022
IRF3#3661	5	29.363720132181	2.31300241196823e-07	1.22003868133106e-05
MAX#4149	6	4.83941663175534	0.000291750431370536	0.00309718675563198
MXI1#4601	7	8.71637517516439	7.48926294096089e-07	3.31428445886023e-05
NFYA#4800	6	13.8191855248729	6.49659712753933e-07	2.94614896831559e-05
NFYB#4801	6	12.5698449401523	1.13616741401493e-06	4.66065155350768e-05
PAX5#5079	5	4.16847845698614	0.00284750870610728	0.0154360511656358
POLR2A#5430	8	2.14745317655807	0.00221072578897191	0.0127167873250957
POU2F2#5452	4	4.55306202887126	0.00706247384683113	0.0294591303654124
RFX5#5993	5	7.52994426699694	0.00017791725685856	0.00215863155077267
SIN3A#25942	8	5.40888472681514	1.36410592556506e-06	5.35183541548044e-05
SMARCB1#6598	3	6.84476841793403	0.00747369013463395	0.0308223315420563
SP1#6667	8	5.6983813781409	8.98832477855329e-07	3.86309321624414e-05
SREBF1#6720	3	17.6271935401831	0.000497260515006821	0.00439554726422322
TAF1#6872	8	3.34304628574529	6.40776711117462e-05	0.00104337510028682
TAF7#6879	8	11.4330694049239	3.41987905000906e-09	2.81678823425785e-07
TBP#6908	8	3.70677068709639	2.80450451364125e-05	0.000592075291894437
TFAP2C#7022	6	8.10692145739517	1.48721435420767e-05	0.000352606537886709

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.