Coexpression cluster:C3829

Full id: C3829_Alveolar_Osteoblast_Mesenchymal_CD19_CD8_Bronchial_CD4

Phase1 CAGE Peaks

Hg19::chr19:58898627..58898649,+	p1@RPS5
Hg19::chr6:34393834..34393854,-	p1@RPS10
Hg19::chr9:127624220..127624249,-	p1@RPL35

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
3.23952687815502e-08	1.05948726550059e-05	3	92	Ribosome (KEGG):03010
3.34751110742684e-08	1.05948726550059e-05	3	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.1037505066909e-06	0.00011644567845589	3	296	Metabolism of proteins (Reactome):REACT_17015
6.2031341872007e-08	1.30886131349935e-05	3	114	Regulation of beta-cell development (Reactome):REACT_13698
3.18533613032144e-06	0.000252039721311684	3	421	Gene Expression (Reactome):REACT_71
1.29326205516739e-06	0.000116947840131565	3	312	Diabetes pathways (Reactome):REACT_15380
1.23098667822397e-07	1.55842913463155e-05	3	143	Influenza Infection (Reactome):REACT_6167
1.10547371417187e-07	1.55842913463155e-05	3	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)	4.85723043455606e-07
GO:0044445	cytosolic part	4.04684082958443e-06
GO:0033279	ribosomal subunit	4.43156848706747e-06
GO:0005843	cytosolic small ribosomal subunit (sensu Eukaryota)	3.42491428310507e-05
GO:0005829	cytosol	4.37069685763082e-05
GO:0003735	structural constituent of ribosome	9.37311511897516e-05
GO:0005840	ribosome	0.000104438776913281
GO:0003723	RNA binding	0.000139325905542654
GO:0030529	ribonucleoprotein complex	0.000176986787891312
GO:0015935	small ribosomal subunit	0.000176986787891312
GO:0006412	translation	0.000191170908466735
GO:0009059	macromolecule biosynthetic process	0.000381477014010147
GO:0044249	cellular biosynthetic process	0.000670221350290751
GO:0009058	biosynthetic process	0.00126397184777576
GO:0043232	intracellular non-membrane-bound organelle	0.00186361035824562
GO:0043228	non-membrane-bound organelle	0.00186361035824562
GO:0032991	macromolecular complex	0.00412563219299036
GO:0044446	intracellular organelle part	0.00444174770396845
GO:0044422	organelle part	0.00444174770396845
GO:0044444	cytoplasmic part	0.00580049058691586
GO:0003729	mRNA binding	0.00671329398745446
GO:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	0.00734943622756971
GO:0010467	gene expression	0.00845184466754722
GO:0044267	cellular protein metabolic process	0.00867222765158901
GO:0044260	cellular macromolecule metabolic process	0.00867222765158901
GO:0019538	protein metabolic process	0.00926456805294909
GO:0003676	nucleic acid binding	0.0115094352670833
GO:0015934	large ribosomal subunit	0.0155166873431472
GO:0005737	cytoplasm	0.0173082764382631
GO:0005730	nucleolus	0.0227175953065135
GO:0043234	protein complex	0.0308951312220169
GO:0043229	intracellular organelle	0.0453464256071891
GO:0043226	organelle	0.0453464256071891
GO:0043170	macromolecule metabolic process	0.0487865755901209

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
animal cell	1.75e-27	679
eukaryotic cell	1.75e-27	679
native cell	3.52e-27	722
somatic cell	1.29e-17	588
lymphocyte	9.00e-13	53
common lymphoid progenitor	9.00e-13	53
lymphoid lineage restricted progenitor cell	1.36e-12	52
nucleate cell	7.75e-12	55
contractile cell	8.80e-11	59
embryonic cell	7.11e-10	250
smooth muscle cell	3.91e-09	43
smooth muscle myoblast	3.91e-09	43
mesodermal cell	4.33e-09	121
muscle cell	4.35e-09	55
electrically responsive cell	9.26e-09	61
electrically active cell	9.26e-09	61
muscle precursor cell	2.10e-08	58
myoblast	2.10e-08	58
multi-potent skeletal muscle stem cell	2.10e-08	58
lymphocyte of B lineage	6.81e-08	24
pro-B cell	6.81e-08	24
B cell	8.46e-08	14
epithelial cell	1.01e-07	253
mature alpha-beta T cell	1.32e-07	18
alpha-beta T cell	1.32e-07	18
immature T cell	1.32e-07	18
mature T cell	1.32e-07	18
immature alpha-beta T cell	1.32e-07	18
vascular associated smooth muscle cell	2.62e-07	32
T cell	7.07e-07	25
pro-T cell	7.07e-07	25

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	9.60e-11	78
multilaminar epithelium	4.75e-09	83
somite	6.83e-09	71
presomitic mesoderm	6.83e-09	71
presumptive segmental plate	6.83e-09	71
dermomyotome	6.83e-09	71
trunk paraxial mesoderm	6.83e-09	71
dense mesenchyme tissue	2.31e-08	73
paraxial mesoderm	2.57e-08	72
presumptive paraxial mesoderm	2.57e-08	72
skeletal muscle tissue	7.55e-08	62
striated muscle tissue	7.55e-08	62
myotome	7.55e-08	62
unilaminar epithelium	2.97e-07	148
muscle tissue	6.38e-07	64
musculature	6.38e-07	64
musculature of body	6.38e-07	64

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325400224142118
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462310027584088
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255711240639509
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154115289571078
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.0155804852863607
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00433901022793572
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128084721540172
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186513583291039
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294513355426656
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269616091599555
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381337945942531
NR2C2#7182	2	21.7430739368272	0.00276220797549601	0.0151378621374208
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172908494235542
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00882261490006564
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276776576924785
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370766150895037
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246520686906664
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00543071596465444
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0390149672603868
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190274081051498
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329404107922251

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.