Coexpression cluster:C4341

Full id: C4341_CD8_CD4_CD133_CD19_CD34_skeletal_neuroectodermal

Phase1 CAGE Peaks

Hg19::chr3:61728802..61728813,-	p1@RPL10AP6
Hg19::chr5:149829294..149829310,-	p1@RPS14
Hg19::chr6:33239845..33239859,+	p1@RPS18

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
3.0758227865789e-05	0.00943346997452502	2	92	Ribosome (KEGG):03010
3.14334971571015e-05	0.00943346997452502	2	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
0.00031927672820075	0.0320708702750472	2	296	Metabolism of proteins (Reactome):REACT_17015
4.73033289875392e-05	0.00943346997452502	2	114	Regulation of beta-cell development (Reactome):REACT_13698
0.000354654173657709	0.0320708702750472	2	312	Diabetes pathways (Reactome):REACT_15380
7.45139808414298e-05	0.00943346997452502	2	143	Influenza Infection (Reactome):REACT_6167
6.93847325306698e-05	0.00943346997452502	2	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:0005843	cytosolic small ribosomal subunit (sensu Eukaryota)	7.194409102925e-05
GO:0005830	cytosolic ribosome (sensu Eukaryota)	0.000177936588775551
GO:0015935	small ribosomal subunit	0.000310347059341862
GO:0044445	cytosolic part	0.000575648910173879
GO:0033279	ribosomal subunit	0.000622361272308287
GO:0042257	ribosomal subunit assembly	0.000622361272308287
GO:0000028	ribosomal small subunit assembly and maintenance	0.000622361272308287
GO:0042274	ribosomal small subunit biogenesis and assembly	0.000968103285525504
GO:0030490	maturation of SSU-rRNA	0.000968103285525504
GO:0005829	cytosol	0.00206506472197114
GO:0042255	ribosome assembly	0.00277209174988996
GO:0003735	structural constituent of ribosome	0.00323014220823884
GO:0005840	ribosome	0.00355109640920681
GO:0003723	RNA binding	0.00436735624453293
GO:0030529	ribonucleoprotein complex	0.00553112840447372
GO:0006412	translation	0.00583360297203652
GO:0009059	macromolecule biosynthetic process	0.00870856932178837
GO:0019843	rRNA binding	0.00870856932178837
GO:0044249	cellular biosynthetic process	0.0126687003930597
GO:0006364	rRNA processing	0.0153350836109307
GO:0016072	rRNA metabolic process	0.0153350836109307
GO:0009058	biosynthetic process	0.0175449323810289
GO:0042254	ribosome biogenesis and assembly	0.0209909472866491
GO:0043234	protein complex	0.0210206369465923
GO:0043232	intracellular non-membrane-bound organelle	0.0210206369465923
GO:0043228	non-membrane-bound organelle	0.0210206369465923
GO:0022618	protein-RNA complex assembly	0.0223825016040295
GO:0045892	negative regulation of transcription, DNA-dependent	0.0314909289356775
GO:0032991	macromolecular complex	0.0333293770674674
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.0341701770605187
GO:0044446	intracellular organelle part	0.0341701770605187
GO:0044422	organelle part	0.0341701770605187
GO:0016481	negative regulation of transcription	0.0382526883561942
GO:0044444	cytoplasmic part	0.0395208036809799
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0395208036809799
GO:0031324	negative regulation of cellular metabolic process	0.0458487231224755

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
lymphoid lineage restricted progenitor cell	2.00e-16	52
lymphocyte	3.01e-16	53
common lymphoid progenitor	3.01e-16	53
nucleate cell	2.77e-14	55
native cell	8.51e-11	722
animal cell	1.23e-09	679
eukaryotic cell	1.23e-09	679
T cell	4.03e-09	25
pro-T cell	4.03e-09	25
mature alpha-beta T cell	4.13e-09	18
alpha-beta T cell	4.13e-09	18
immature T cell	4.13e-09	18
mature T cell	4.13e-09	18
immature alpha-beta T cell	4.13e-09	18
lymphocyte of B lineage	2.78e-08	24
pro-B cell	2.78e-08	24
somatic cell	6.54e-08	588
B cell	2.65e-07	14

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	2	23.0314018691589	0.00246467476084291	0.013860013318311
BCLAF1#9774	2	14.4350984067479	0.00620114743554613	0.0273948494996405
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0402105153900584
JUNB#3726	2	20.4070884398808	0.00313146219943874	0.0164535282309797
NR2C2#7182	2	21.7430739368272	0.00276220797549601	0.0151402455522634
RDBP#7936	2	102.425602660017	0.000126437939273122	0.00168367358660533
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.0048584496358714
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370872827003908
SP2#6668	2	17.4356869958964	0.00427356848176974	0.0203254801524454
STAT1#6772	2	13.8043916647995	0.00677093170844408	0.0287611069548213
THAP1#55145	2	20.9127630685675	0.00298344741373694	0.0158746823131889
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329319677657193
WRNIP1#56897	2	73.2133095662507	0.00024709364113596	0.00268590890784747
ZZZ3#26009	1	79.8044041450777	0.012478437908258	0.0451665480245566

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.