Coexpression cluster:C3402

Full id: C3402_CD8_CD4_diffuse_non_cord_CD19_b

Phase1 CAGE Peaks

Hg19::chr14:20811696..20811707,+	p4@PARP2
Hg19::chr1:186344883..186344903,+	p3@C1orf27
Hg19::chr1:186344904..186344925,+	p2@C1orf27

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:0006471	protein amino acid ADP-ribosylation	0.0320481603041205
GO:0006284	base-excision repair	0.0320481603041205
GO:0003950	NAD+ ADP-ribosyltransferase activity	0.0320481603041205

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
nucleate cell	1.28e-29	55
lymphocyte	2.56e-28	53
common lymphoid progenitor	2.56e-28	53
lymphoid lineage restricted progenitor cell	1.15e-27	52
hematopoietic stem cell	1.59e-22	168
angioblastic mesenchymal cell	1.59e-22	168
hematopoietic cell	1.34e-20	177
leukocyte	4.91e-20	136
hematopoietic oligopotent progenitor cell	6.81e-20	161
hematopoietic multipotent progenitor cell	6.81e-20	161
hematopoietic lineage restricted progenitor cell	4.64e-16	120
nongranular leukocyte	2.73e-15	115
lymphocyte of B lineage	5.58e-14	24
pro-B cell	5.58e-14	24
T cell	5.37e-13	25
pro-T cell	5.37e-13	25
mature alpha-beta T cell	2.32e-12	18
alpha-beta T cell	2.32e-12	18
immature T cell	2.32e-12	18
mature T cell	2.32e-12	18
immature alpha-beta T cell	2.32e-12	18
B cell	2.57e-09	14
CD8-positive, alpha-beta T cell	2.77e-08	11

Uber Anatomy

Ontology term	p-value	n
adult organism	2.82e-10	114
blood	9.72e-07	15
haemolymphatic fluid	9.72e-07	15
organism substance	9.72e-07	15

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
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.00129419891273341
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139055182331537
BDP1#55814	1	350.051136363636	0.00285402147532321	0.0154705532185229
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164040051552855
BRF2#55290	1	358.191860465116	0.00278921773335872	0.0152770668583098
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189574510729739
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00659216538198562
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.0306705681090718
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324301544583211
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436240568159385
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00913507429655453
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319673099266817
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460923743383747
ELK4#2005	2	10.823787772312	0.0109128471951648	0.040180745574328
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167148150522557
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00433156703344574
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00390409840064717
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108497301166698
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127791477696907
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156385268497002
MEF2C#4208	3	41.3113544926241	1.41744912101957e-05	0.000340236655366957
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293734687740154
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269042025058654
POLR3A#11128	1	113.044036697248	0.0088200988100312	0.0334955928737446
REST#5978	3	9.65002871612802	0.00111263624711459	0.00766204780511675
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00483641228129431
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275897186462984
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370632892026153
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00202733944121467
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457221169214158
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245865589459428
SP2#6668	2	17.4356869958964	0.00427356848176974	0.0203106811680341
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0108932854489801
SREBF2#6721	1	145.647754137116	0.00685021551456999	0.0290459038661108
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00374349403653057
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154591198304815
STAT2#6773	2	43.5091807909604	0.000696899089886823	0.00560692119626299
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00641893268817205
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00541598260609597
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.0019671211407341
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189855524381582
USF2#7392	3	12.9921973850696	0.000455897939342781	0.0042091164150478
WRNIP1#56897	2	73.2133095662507	0.00024709364113596	0.0026847911763003
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328520328828109

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.