Coexpression cluster:C3036

Full id: C3036_Mast_CD14_diffuse_Reticulocytes_chronic_acute_teratocarcinoma

Phase1 CAGE Peaks

Hg19::chr10:70091812..70091830,+	p1@HNRNPH3
Hg19::chr10:70091847..70091858,+	p2@HNRNPH3
Hg19::chr7:26240357..26240377,-	p1@HNRNPA2B1

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:0043047	single-stranded telomeric DNA binding	0.00565171317555634
GO:0042162	telomeric DNA binding	0.00847756976333451
GO:0030530	heterogeneous nuclear ribonucleoprotein complex	0.00847756976333451
GO:0003697	single-stranded DNA binding	0.0118172184579814
GO:0000375	RNA splicing, via transesterification reactions	0.0118172184579814
GO:0000398	nuclear mRNA splicing, via spliceosome	0.0118172184579814
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0118172184579814
GO:0050658	RNA transport	0.0118172184579814
GO:0051236	establishment of RNA localization	0.0118172184579814
GO:0050657	nucleic acid transport	0.0118172184579814
GO:0006403	RNA localization	0.0118172184579814
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0122453785470387
GO:0005681	spliceosome	0.0151074640654294
GO:0043566	structure-specific DNA binding	0.0160468284805975
GO:0008380	RNA splicing	0.0211939244083363
GO:0006397	mRNA processing	0.0241080890144825
GO:0016071	mRNA metabolic process	0.0284247927358863
GO:0006396	RNA processing	0.041210408571765

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><br>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	1.29e-17	172
angioblastic mesenchymal cell	1.29e-17	172
hematopoietic oligopotent progenitor cell	3.34e-17	165
hematopoietic multipotent progenitor cell	3.34e-17	165
myeloid cell	1.20e-16	112
common myeloid progenitor	1.20e-16	112
hematopoietic cell	8.40e-16	182
classical monocyte	1.95e-13	45
CD14-positive, CD16-negative classical monocyte	1.38e-12	42
leukocyte	2.35e-10	140
hematopoietic lineage restricted progenitor cell	3.34e-09	124
myeloid leukocyte	7.03e-09	76
myeloid lineage restricted progenitor cell	1.96e-08	70
nongranular leukocyte	1.02e-07	119
granulocyte monocyte progenitor cell	2.13e-07	71
macrophage dendritic cell progenitor	4.67e-07	65
monopoietic cell	8.82e-07	63
monocyte	8.82e-07	63
monoblast	8.82e-07	63
promonocyte	8.82e-07	63

Disease

Ontology term	p-value	n
cancer	5.42e-26	235
disease of cellular proliferation	2.65e-24	239
hematologic cancer	1.22e-13	51
immune system cancer	1.22e-13	51
cell type cancer	3.46e-13	143
organ system cancer	1.09e-12	137
leukemia	3.62e-12	39
carcinoma	1.51e-10	106
myeloid leukemia	7.53e-10	31

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
BCL3#602	3	34.5471028037383	2.42397750207122e-05	0.000526206165742707
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00138811192944263
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296072306613639
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189076825251128
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323435031177605
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435205596467429
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320286803243479
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0318946046237894
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0459873838889061
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0166799614015659
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00759622569692998
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376563918118052
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.00062572471085838
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00432674263561891
HNF4G#3174	2	19.1689483509645	0.00354398661128422	0.0179657517569125
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127582838549647
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156121239342167
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185640650908284
MEF2A#4205	2	12.495487273096	0.00823502947802974	0.0324685055553606
MEF2C#4208	2	27.5409029950827	0.00172911993836969	0.0106447130706391
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293100651958966
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174417285193353
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268470397928542
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00307821802712234
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00469238378100564
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172214796083612
PBX3#5090	2	14.6096751244961	0.00605612247321789	0.0268051947355655
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.008792884572643
RDBP#7936	3	153.638403990025	2.75057764221434e-07	1.39653659881003e-05
REST#5978	3	9.65002871612802	0.00111263624711459	0.00765195686898463
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.029815471889042
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275321681276369
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245363212157255
STAT2#6773	2	43.5091807909604	0.000696899089886823	0.00560605746350535
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00540383539066079
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00627579423211213
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0328898315031959
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189447652434937
WRNIP1#56897	2	73.2133095662507	0.00024709364113596	0.00268451188875465
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327799648426515
ZBTB33#10009	3	31.6647250299812	3.14815888737575e-05	0.000632898105945402
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00241840653976096

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.