Coexpression cluster:C1115

Full id: C1115_CD4_CD34_CD8_CD19_Basophils_Peripheral_Dendritic

Phase1 CAGE Peaks

Hg19::chr10:32667648..32667659,-	p5@EPC1
Hg19::chr10:32667660..32667735,-	p2@EPC1
Hg19::chr13:103249302..103249321,+	p2@TPP2
Hg19::chr16:10479876..10479887,+	p2@ATF7IP2
Hg19::chr2:242823508..242823531,+	p1@ENST00000415434 p1@ENST00000430555 p1@ENST00000457686
Hg19::chr4:89205879..89205911,-	p3@PPM1K
Hg19::chr9:100396030..100396055,+	p3@NCBP1

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:0031442	positive regulation of mRNA 3'-end processing	0.00520005491694157
GO:0050685	positive regulation of mRNA processing	0.00520005491694157
GO:0004294	tripeptidyl-peptidase II activity	0.00520005491694157
GO:0008717	D-alanyl-D-alanine endopeptidase activity	0.00520005491694157
GO:0031974	membrane-enclosed lumen	0.00520005491694157
GO:0043233	organelle lumen	0.00520005491694157
GO:0051254	positive regulation of RNA metabolic process	0.00520005491694157
GO:0008240	tripeptidyl-peptidase activity	0.00520005491694157
GO:0031440	regulation of mRNA 3'-end processing	0.00520005491694157
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0112746726374699
GO:0000339	RNA cap binding	0.0133668470752712
GO:0031325	positive regulation of cellular metabolic process	0.0133668470752712
GO:0006379	mRNA cleavage	0.0133668470752712
GO:0050684	regulation of mRNA processing	0.0133668470752712
GO:0009893	positive regulation of metabolic process	0.0136880817127755
GO:0031124	mRNA 3'-end processing	0.0204607554870117
GO:0005654	nucleoplasm	0.0211322557389912
GO:0031123	RNA 3'-end processing	0.0233768379318203
GO:0051252	regulation of RNA metabolic process	0.0233768379318203
GO:0006406	mRNA export from nucleus	0.025709980262606
GO:0043170	macromolecule metabolic process	0.0273417798653032
GO:0045814	negative regulation of gene expression, epigenetic	0.0273417798653032
GO:0031981	nuclear lumen	0.0273417798653032
GO:0006405	RNA export from nucleus	0.0292021291118577
GO:0004289	subtilase activity	0.0323355491475181
GO:0015071	protein phosphatase type 2C activity	0.0323355491475181
GO:0051168	nuclear export	0.0380395566131108
GO:0044237	cellular metabolic process	0.0396635721962796
GO:0048522	positive regulation of cellular process	0.0396635721962796
GO:0044238	primary metabolic process	0.0396635721962796
GO:0044424	intracellular part	0.0413916159462054
GO:0008287	protein serine/threonine phosphatase complex	0.0415469369327996
GO:0048518	positive regulation of biological process	0.0432967094918313
GO:0040029	regulation of gene expression, epigenetic	0.0432967094918313
GO:0004722	protein serine/threonine phosphatase activity	0.0432967094918313
GO:0044428	nuclear part	0.043958325953636
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0472815342760447
GO:0051028	mRNA transport	0.0475876790435889
GO:0043283	biopolymer metabolic process	0.0475876790435889
GO:0004177	aminopeptidase activity	0.0475876790435889
GO:0031323	regulation of cellular metabolic process	0.0475876790435889
GO:0050658	RNA transport	0.0475876790435889
GO:0051236	establishment of RNA localization	0.0475876790435889
GO:0050657	nucleic acid transport	0.0475876790435889
GO:0006403	RNA localization	0.0475876790435889
GO:0044446	intracellular organelle part	0.0483810973952469
GO:0044422	organelle part	0.0483810973952469
GO:0019222	regulation of metabolic process	0.0483810973952469
GO:0016070	RNA metabolic process	0.0483810973952469
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0483810973952469

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
hematopoietic stem cell	8.80e-24	172
angioblastic mesenchymal cell	8.80e-24	172
lymphocyte	1.24e-23	53
common lymphoid progenitor	1.24e-23	53
lymphoid lineage restricted progenitor cell	2.43e-23	52
hematopoietic cell	3.84e-22	182
hematopoietic oligopotent progenitor cell	1.58e-20	165
hematopoietic multipotent progenitor cell	1.58e-20	165
leukocyte	3.71e-19	140
hematopoietic lineage restricted progenitor cell	1.36e-14	124
nongranular leukocyte	2.43e-14	119
T cell	3.35e-12	25
pro-T cell	3.35e-12	25
mature alpha-beta T cell	9.14e-12	18
alpha-beta T cell	9.14e-12	18
immature T cell	9.14e-12	18
mature T cell	9.14e-12	18
immature alpha-beta T cell	9.14e-12	18
lymphocyte of B lineage	1.25e-10	24
pro-B cell	1.25e-10	24
B cell	4.31e-09	14
CD8-positive, alpha-beta T cell	2.77e-08	11

Uber Anatomy

Ontology term	p-value	n
adult organism	1.30e-25	115
neural tube	1.80e-15	57
neural rod	1.80e-15	57
future spinal cord	1.80e-15	57
neural keel	1.80e-15	57
central nervous system	2.89e-15	82
regional part of nervous system	2.47e-14	94
nervous system	2.47e-14	94
regional part of brain	5.50e-14	59
anterior neural tube	1.00e-13	42
regional part of forebrain	1.19e-13	41
forebrain	1.19e-13	41
future forebrain	1.19e-13	41
brain	2.48e-13	69
future brain	2.48e-13	69
telencephalon	2.94e-11	34
gray matter	3.12e-11	34
brain grey matter	3.12e-11	34
cerebral hemisphere	4.28e-11	32
regional part of telencephalon	4.91e-11	33
neurectoderm	9.34e-09	90
regional part of cerebral cortex	1.11e-08	22
cerebral cortex	1.27e-08	25
pallium	1.27e-08	25
neocortex	4.38e-08	20
neural plate	7.21e-08	86
presumptive neural plate	7.21e-08	86
blood	8.89e-08	15
haemolymphatic fluid	8.89e-08	15
organism substance	8.89e-08	15
pre-chordal neural plate	6.59e-07	61

Disease

Ontology term	p-value	n
hematologic cancer	8.37e-07	51
immune system cancer	8.37e-07	51

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
CHD2#1106	5	7.3885877386549	0.000149868960082067	0.00193141218188685
E2F1#1869	5	3.50527801062809	0.00509055358791505	0.0236837280010807
E2F4#1874	3	5.42916870655047	0.0135067508217614	0.0477032075030923
EGR1#1958	5	3.56298506772153	0.00472235121105893	0.0222552068106937
ELF1#1997	5	3.04149854200538	0.00971956226937075	0.0365565169926106
EP300#2033	4	3.87082384355611	0.0114256758668448	0.041859408631473
FOS#2353	4	5.14168874793966	0.00404209586567825	0.0193479284163147
GTF2B#2959	4	18.2536171053281	3.11241110089347e-05	0.0006292239701243
GTF2F1#2962	3	5.45985466146756	0.013298821684157	0.0470213161985129
HEY1#23462	6	3.46295232266204	0.00126789009587212	0.00850354313657776
IRF1#3659	4	4.36409357346509	0.0073934558242782	0.0305493405931236
NANOG#79923	3	12.5334764918626	0.00126105218950347	0.00846747007969353
NFKB1#4790	5	3.9200453029956	0.00303658142448461	0.0161155306363
NFYA#4800	6	15.793354885569	1.7032585757508e-07	9.38220582240704e-06
NFYB#4801	6	14.3655370744598	2.99325254948281e-07	1.50947514734638e-05
PAX5#5079	4	3.81118030353019	0.0120826168155519	0.0438204124596112
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223219917594188
REST#5978	5	6.89287765437716	0.000209438858484651	0.00243825492601477
RFX5#5993	6	10.3267807090244	2.12421369818918e-06	7.73538195345816e-05
SP1#6667	6	4.88432689554934	0.000173636112229091	0.00211282557673238
SP2#6668	4	14.9448745679112	6.81071539656055e-05	0.00108762126192873
TAF1#6872	6	2.86546824492454	0.00372833020747146	0.0185818696510671
TBP#6908	6	3.17723201751119	0.00207411205185266	0.0120149863322114
TCF7L2#6934	4	6.15438660750705	0.00206467614813804	0.0119689560521419
TRIM28#10155	3	7.96736787654108	0.00462234126315646	0.0218311716719937
YY1#7528	5	3.50797910703847	0.00507257067280898	0.0236095284325281

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.