Coexpression cluster:C3081

Full id: C3081_Mast_CD19_pituitary_CD4_CD8_Peripheral_spinal

Phase1 CAGE Peaks

Hg19::chr11:108093755..108093832,+	p1@ATM
Hg19::chr11:108094037..108094072,+	p2@ATM
Hg19::chr15:62352570..62352658,-	p1@VPS13C

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0007094	mitotic cell cycle spindle assembly checkpoint	0.0123605750498787
GO:0031577	spindle checkpoint	0.0123605750498787
GO:0010212	response to ionizing radiation	0.0123605750498787
GO:0035004	phosphoinositide 3-kinase activity	0.0123605750498787
GO:0016303	1-phosphatidylinositol-3-kinase activity	0.0123605750498787
GO:0007131	meiotic recombination	0.0151058126866206
GO:0007093	mitotic cell cycle checkpoint	0.0158893604484329
GO:0007127	meiosis I	0.0160630702308775
GO:0001727	lipid kinase activity	0.0160630702308775
GO:0047485	protein N-terminus binding	0.0160630702308775
GO:0000075	cell cycle checkpoint	0.0182682777581781
GO:0004428	inositol or phosphatidylinositol kinase activity	0.0182682777581781
GO:0007088	regulation of mitosis	0.0182682777581781
GO:0051327	M phase of meiotic cell cycle	0.0182682777581781
GO:0007126	meiosis	0.0182682777581781
GO:0051321	meiotic cell cycle	0.0182682777581781
GO:0009314	response to radiation	0.0244477946042987
GO:0009628	response to abiotic stimulus	0.0376850227570919
GO:0006310	DNA recombination	0.042605422489093
GO:0045786	negative regulation of progression through cell cycle	0.0457285926147825
GO:0007067	mitosis	0.0457285926147825
GO:0000087	M phase of mitotic cell cycle	0.0457285926147825

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>

---

Cell Type

Ontology term	p-value	n
lymphocyte	2.37e-17	53
common lymphoid progenitor	2.37e-17	53
lymphoid lineage restricted progenitor cell	3.95e-17	52
leukocyte	8.02e-17	136
nucleate cell	4.74e-16	55
nongranular leukocyte	1.83e-15	115
hematopoietic stem cell	3.06e-14	168
angioblastic mesenchymal cell	3.06e-14	168
hematopoietic lineage restricted progenitor cell	1.92e-13	120
hematopoietic oligopotent progenitor cell	2.41e-12	161
hematopoietic multipotent progenitor cell	2.41e-12	161
hematopoietic cell	1.04e-11	177
mature alpha-beta T cell	5.31e-11	18
alpha-beta T cell	5.31e-11	18
immature T cell	5.31e-11	18
mature T cell	5.31e-11	18
immature alpha-beta T cell	5.31e-11	18
lymphocyte of B lineage	6.63e-10	24
pro-B cell	6.63e-10	24
B cell	1.58e-08	14
CD8-positive, alpha-beta T cell	4.77e-08	11
T cell	3.70e-07	25
pro-T cell	3.70e-07	25

Uber Anatomy

Ontology term	p-value	n
adult organism	1.17e-21	114
neural tube	2.45e-12	56
neural rod	2.45e-12	56
future spinal cord	2.45e-12	56
neural keel	2.45e-12	56
regional part of nervous system	2.77e-11	53
regional part of brain	2.77e-11	53
regional part of forebrain	1.97e-10	41
forebrain	1.97e-10	41
anterior neural tube	1.97e-10	41
future forebrain	1.97e-10	41
brain	2.03e-09	68
future brain	2.03e-09	68
nervous system	6.28e-09	89
central nervous system	8.44e-09	81
brain grey matter	1.01e-07	34
gray matter	1.01e-07	34
neurectoderm	2.77e-07	86
telencephalon	2.88e-07	34
regional part of telencephalon	4.87e-07	32

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189129090106537
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278240120578471
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171061781112348
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323577153568543
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320410906933514
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319066991991274
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460061529728686
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0401736640188867
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00759826153631275
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127603671802186
IRF4#3662	2	14.6096751244961	0.00605612247321789	0.0268074669399171
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185738225791693
MEF2A#4205	3	18.7432309096441	0.000151824390562247	0.00194795915551971
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268595947387653
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00469430389876528
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172273796845778
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00661692824914584
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00482937124109184
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.0298166547141259
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275402107423718
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.0030800067411172
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.032891069265935
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189500753710963
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00420391355174119
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327921575020685
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.0377929742186717
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00387644150859182

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.