Coexpression cluster:C527

Full id: C527_CD4_CD8_CD19_CD34_CD133_skeletal_Mesenchymal

Phase1 CAGE Peaks

Hg19::chr11:118889041..118889062,-	p1@RPS25
Hg19::chr11:17099202..17099230,-	p1@RPS13
Hg19::chr11:64889592..64889615,-	p1@FAU
Hg19::chr11:75110555..75110574,+	p1@RPS3
Hg19::chr11:809961..809977,+	p1@RPLP2
Hg19::chr17:17287371..17287378,-	p1@ENST00000392730 p1@ENST00000396469
Hg19::chr19:39926576..39926593,-	p1@RPS16
Hg19::chr19:49999681..49999705,+	p1@RPS11
Hg19::chr1:153963227..153963249,+	p1@RPS27
Hg19::chr2:207024612..207024634,+	p1@EEF1B2
Hg19::chr3:23958632..23958651,+	p2@RPL15
Hg19::chr5:81574161..81574189,-	p1@RPS23
Hg19::chr6:133135704..133135711,+	p1@RPS12
Hg19::chr6:153603882..153603892,-	p1@ENST00000492974
Hg19::chr8:56987061..56987067,-	p1@RPS20
Hg19::chr8:99057769..99057776,-	p1@RPL30
Hg19::chr9:19380220..19380245,-	p1@RPS6

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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p.value	FDR	nGenes	nPathway	Name
6.91014427352572e-35	1.7163710643638e-32	14	92	Ribosome (KEGG):03010
0.000120664641274534	0.00763807179267799	3	188	TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231
8.13446002068154e-35	1.7163710643638e-32	14	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.20547531912621e-30	1.27177646167815e-28	15	296	Metabolism of proteins (Reactome):REACT_17015
1.71339533049491e-33	2.7114481105082e-31	14	114	Regulation of beta-cell development (Reactome):REACT_13698
2.64892183772546e-28	2.3953821761146e-26	15	421	Gene Expression (Reactome):REACT_71
3.84782720500134e-27	3.04459327595731e-25	14	312	Diabetes pathways (Reactome):REACT_15380
4.86641825718034e-32	6.16088551359031e-30	14	143	Influenza Infection (Reactome):REACT_6167
2.93027540557533e-13	2.06096036858798e-11	10	728	TNF alpha/NF-kB up reg. targets (Netpath):NetPath_9
8.39347489466827e-36	5.31306960832501e-33	15	138	{RPS27A,138} (Static Module):NA

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:0005830	cytosolic ribosome (sensu Eukaryota)	1.53717595287726e-28
GO:0005843	cytosolic small ribosomal subunit (sensu Eukaryota)	2.22911714947442e-26
GO:0044445	cytosolic part	6.2977514458212e-24
GO:0033279	ribosomal subunit	3.58722918760839e-23
GO:0003735	structural constituent of ribosome	1.77922535769504e-21
GO:0006412	translation	1.77922535769504e-21
GO:0005840	ribosome	4.47164198772868e-21
GO:0015935	small ribosomal subunit	5.31479479118266e-21
GO:0009059	macromolecule biosynthetic process	5.89884984362245e-20
GO:0030529	ribonucleoprotein complex	1.92857280141859e-19
GO:0005829	cytosol	1.07577653929725e-18
GO:0044249	cellular biosynthetic process	1.1174865310891e-18
GO:0009058	biosynthetic process	3.59966244039392e-17
GO:0003723	RNA binding	5.75583651685696e-16
GO:0032991	macromolecular complex	3.09290771796598e-14
GO:0043232	intracellular non-membrane-bound organelle	6.0665711660925e-14
GO:0043228	non-membrane-bound organelle	6.0665711660925e-14
GO:0044444	cytoplasmic part	3.20273086792488e-13
GO:0010467	gene expression	4.02078380200549e-12
GO:0044267	cellular protein metabolic process	5.4410593064807e-12
GO:0044260	cellular macromolecule metabolic process	6.28142478439238e-12
GO:0019538	protein metabolic process	1.01562353823208e-11
GO:0005737	cytoplasm	3.82952380538418e-10
GO:0043234	protein complex	4.26009319663417e-09
GO:0044446	intracellular organelle part	8.06342440604049e-09
GO:0044422	organelle part	8.06342440604049e-09
GO:0003676	nucleic acid binding	6.04178419965562e-08
GO:0043170	macromolecule metabolic process	1.2447166993263e-07
GO:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	1.3911532841307e-06
GO:0043229	intracellular organelle	2.24095090694968e-06
GO:0043226	organelle	2.24095090694968e-06
GO:0044237	cellular metabolic process	3.93747758510936e-06
GO:0044238	primary metabolic process	4.42357966828784e-06
GO:0044424	intracellular part	5.74349273900959e-06
GO:0015934	large ribosomal subunit	2.32336017423447e-05
GO:0005622	intracellular	6.70743009689029e-05
GO:0006414	translational elongation	0.000567391746485201
GO:0043284	biopolymer biosynthetic process	0.00150908021917965
GO:0005515	protein binding	0.0104877819644371
GO:0042593	glucose homeostasis	0.0109937085211293
GO:0033500	carbohydrate homeostasis	0.0109937085211293
GO:0044464	cell part	0.0127976687206917
GO:0005853	eukaryotic translation elongation factor 1 complex	0.0156976823336595
GO:0019843	rRNA binding	0.0229546190419338
GO:0003746	translation elongation factor activity	0.0329280001100885

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><br>

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Cell Type

Ontology term	p-value	n
lymphocyte	2.23e-20	53
common lymphoid progenitor	2.23e-20	53
lymphoid lineage restricted progenitor cell	4.93e-20	52
nucleate cell	2.60e-19	55
nongranular leukocyte	1.60e-17	115
hematopoietic stem cell	4.65e-15	168
angioblastic mesenchymal cell	4.65e-15	168
hematopoietic cell	1.69e-14	177
hematopoietic lineage restricted progenitor cell	3.05e-14	120
native cell	2.32e-13	722
leukocyte	2.37e-13	136
hematopoietic oligopotent progenitor cell	3.87e-13	161
hematopoietic multipotent progenitor cell	3.87e-13	161
mature alpha-beta T cell	1.04e-11	18
alpha-beta T cell	1.04e-11	18
immature T cell	1.04e-11	18
mature T cell	1.04e-11	18
immature alpha-beta T cell	1.04e-11	18
T cell	1.40e-10	25
pro-T cell	1.40e-10	25
B cell	2.05e-09	14
lymphocyte of B lineage	2.15e-09	24
pro-B cell	2.15e-09	24
somatic cell	2.46e-09	588
animal cell	4.42e-09	679
eukaryotic cell	4.42e-09	679
CD8-positive, alpha-beta T cell	2.69e-08	11
stem cell	4.31e-07	441

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	5	6.6068160370614	0.000688705274230141	0.00555297538294772
BCL3#602	5	10.1609125893348	9.3771989931945e-05	0.00136152549096377
BCLAF1#9774	9	11.4631663818292	1.64938010205014e-08	1.19541713031239e-06
BRCA1#672	9	10.6857691640596	3.02685895110408e-08	2.0487499805208e-06
CCNT2#905	9	3.35445965839198	0.000436791244356075	0.00407194865386986
CEBPB#1051	7	3.28223725769257	0.00300615955226439	0.0159743715009128
CHD2#1106	8	4.86777545134911	8.28678044676969e-05	0.00124527059435997
CTCF#10664	10	3.15309198416178	0.000272288389173733	0.00290415921945624
E2F1#1869	13	3.7527093996136	1.07464925288554e-06	4.47509144027565e-05
E2F4#1874	10	7.45180018546144	1.08332875404144e-07	6.31724018667414e-06
E2F6#1876	11	3.24639488521596	7.30785949477464e-05	0.00114753501394492
EGR1#1958	11	3.22764529664185	7.72881844422271e-05	0.00119160033878975
ELF1#1997	15	3.75714525777136	3.01093513305367e-08	2.04326870929819e-06
ELK4#2005	12	11.4604811706833	1.36979533911823e-11	1.68504187776406e-09
EP300#2033	9	3.58620444329464	0.000260364373300338	0.0027912332973839
ETS1#2113	12	6.86736065096636	5.21732437064727e-09	4.18182762813531e-07
FOSL2#2355	6	5.97536491925707	0.000297459514596548	0.00310477455975904
GABPB1#2553	15	6.23619162016074	1.85944138102383e-11	2.24247342254905e-09
GATA1#2623	7	5.58365629450606	0.000118669714610486	0.00161146097051158
GATA3#2625	4	6.40859208404847	0.00294238410040412	0.0156985774233515
GTF2B#2959	14	26.3066834753258	5.32024204737651e-19	1.25995637003618e-16
GTF2F1#2962	15	11.2408772441979	3.06871838319925e-15	5.52575653832667e-13
HEY1#23462	15	3.56480386156386	6.42357439240872e-08	3.95794504996327e-06
HMGN3#9324	7	3.36763729785024	0.00258933236757512	0.0143204449871414
IRF1#3659	15	6.73867390020344	5.9464769948207e-12	7.68618949086731e-10
IRF4#3662	5	6.44544490786592	0.000770512874507435	0.0060409574431861
JUND#3727	12	4.93740984132072	2.2224306781037e-07	1.18061260218959e-05
KAT2A#2648	3	108.721764705882	2.8307392927591e-06	9.7699795438357e-05
MAX#4149	14	5.31386924271175	1.9579146541289e-09	1.69133704352827e-07
MEF2A#4205	5	5.51271497342472	0.00155536061245248	0.00987779306804042
MEF2C#4208	3	7.29023902811013	0.00747486284700268	0.0308247335101521
MXI1#4601	9	5.27377321522551	1.18160458251851e-05	0.000299020113868792
MYC#4609	15	4.60789576906712	1.5591047504541e-09	1.37526470466787e-07
NFKB1#4790	15	4.84240890370044	7.5609025131929e-10	7.15913959723802e-08
NR2C2#7182	7	13.4295456668639	3.76445247482019e-07	1.84840456990007e-05
NRF1#4899	9	6.4642655899646	2.18388258131197e-06	7.83788704156842e-05
PAX5#5079	14	5.49258337861704	1.25245751600589e-09	1.14041334362807e-07
POLR2A#5430	15	1.89481162637477	0.00045412137082633	0.00422107350015406
POU2F2#5452	13	6.96350663239134	5.21432763147211e-10	5.02843179596783e-08
RDBP#7936	6	54.2253190553029	8.74207406264564e-10	8.18846164151254e-08
REST#5978	11	6.24413622808284	1.00510740280017e-07	5.90064148628705e-06
RFX5#5993	8	5.66960509515063	2.75176813312189e-05	0.00058508125418387
RXRA#6256	7	8.26601882199605	9.47656767003136e-06	0.000251837977325803
SIN3A#25942	16	5.09071503700248	2.6091191843489e-11	3.07208341030682e-09
SIX5#147912	12	12.0612108391475	7.52951998920128e-12	9.53182470487506e-10
SP1#6667	17	5.6983813781409	1.41488962347743e-13	2.17949347177522e-11
SPI1#6688	12	5.79128718248663	3.65832040474177e-08	2.43047916508159e-06
SRF#6722	11	8.92758593434388	2.36843848361268e-09	2.01759662960869e-07
STAT1#6772	6	7.30820735195266	9.87071454255867e-05	0.00139083588250173
STAT2#6773	3	11.5171360917248	0.00208062454216598	0.012052043625029
TAF1#6872	15	2.94974672271643	9.6669521918546e-07	4.10576177293657e-05
TAF7#6879	14	9.41546892170205	8.03861479186331e-13	1.14691924897187e-10
TBP#6908	15	3.27068001802622	2.21275576192132e-07	1.1760712418285e-05
TCF12#6938	10	6.25556758952142	5.62154679880538e-07	2.59667724953753e-05
TCF7L2#6934	7	4.43477858482126	0.000498305774925007	0.0044032961187404
TRIM28#10155	7	7.65492207746104	1.56494839226159e-05	0.00036646108775652
USF1#7391	12	4.49047007802915	6.43363093087209e-07	2.92013029460821e-05
YY1#7528	14	4.04449355870318	7.60115579236282e-08	4.57290961865542e-06
ZBTB33#10009	6	11.1757853046992	9.06703361730025e-06	0.00024224914913206
ZEB1#6935	7	6.95406024251806	2.9174422587585e-05	0.000610121650105084
ZNF143#7702	9	7.14752288059124	9.38784177277639e-07	4.0215619643437e-05
ZNF263#10127	8	3.86910194682855	0.000418295010921723	0.00391384273836712

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.