Coexpression cluster:C2180

Full id: C2180_Eosinophils_CD14_Neutrophils_CD19_Natural_Basophils_CD4

Phase1 CAGE Peaks

Hg19::chr12:105501983..105502018,-	p@chr12:105501983..105502018 -
Hg19::chr14:24711806..24711861,-	p1@TINF2
Hg19::chr15:45003504..45003582,-	p1@PATL2
Hg19::chr16:72127670..72127755,+	p2@DHX38

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:0042162	telomeric DNA binding	0.0150498688801005
GO:0007004	telomere maintenance via telomerase	0.0150498688801005
GO:0004004	ATP-dependent RNA helicase activity	0.0150498688801005
GO:0008186	RNA-dependent ATPase activity	0.0150498688801005
GO:0032200	telomere organization and biogenesis	0.0150498688801005
GO:0000723	telomere maintenance	0.0150498688801005
GO:0003724	RNA helicase activity	0.0150498688801005
GO:0000781	chromosome, telomeric region	0.0150498688801005
GO:0006278	RNA-dependent DNA replication	0.0226427060366972
GO:0000375	RNA splicing, via transesterification reactions	0.0226427060366972
GO:0000398	nuclear mRNA splicing, via spliceosome	0.0226427060366972
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0226427060366972
GO:0005681	spliceosome	0.0414611412249278

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
leukocyte	4.04e-66	140
hematopoietic stem cell	1.70e-58	172
angioblastic mesenchymal cell	1.70e-58	172
hematopoietic cell	7.56e-56	182
hematopoietic lineage restricted progenitor cell	5.03e-55	124
hematopoietic oligopotent progenitor cell	1.93e-54	165
hematopoietic multipotent progenitor cell	1.93e-54	165
nongranular leukocyte	2.43e-54	119
myeloid leukocyte	1.63e-34	76
granulocyte monocyte progenitor cell	2.15e-30	71
myeloid lineage restricted progenitor cell	3.29e-29	70
myeloid cell	7.94e-29	112
common myeloid progenitor	7.94e-29	112
macrophage dendritic cell progenitor	2.72e-28	65
monopoietic cell	1.74e-27	63
monocyte	1.74e-27	63
monoblast	1.74e-27	63
promonocyte	1.74e-27	63
classical monocyte	4.52e-26	45
CD14-positive, CD16-negative classical monocyte	5.97e-26	42
lymphocyte	1.83e-23	53
common lymphoid progenitor	1.83e-23	53
lymphoid lineage restricted progenitor cell	4.18e-23	52
mesenchymal cell	1.83e-20	358
connective tissue cell	2.68e-18	365
motile cell	5.95e-15	390
multi fate stem cell	2.23e-14	430
somatic stem cell	9.43e-13	436
stem cell	4.44e-12	444
lymphocyte of B lineage	2.71e-11	24
pro-B cell	2.71e-11	24
T cell	3.10e-11	25
pro-T cell	3.10e-11	25
mature alpha-beta T cell	4.93e-10	18
alpha-beta T cell	4.93e-10	18
immature T cell	4.93e-10	18
mature T cell	4.93e-10	18
immature alpha-beta T cell	4.93e-10	18
B cell	1.41e-08	14

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	2.61e-39	112
hematopoietic system	1.96e-38	102
blood island	1.96e-38	102
bone marrow	1.46e-28	80
bone element	4.03e-26	86
immune system	1.28e-25	115
lateral plate mesoderm	2.70e-19	216
skeletal element	5.12e-19	101
skeletal system	5.12e-19	101
connective tissue	8.23e-17	375
blood	7.33e-08	15
haemolymphatic fluid	7.33e-08	15
organism substance	7.33e-08	15
musculoskeletal system	5.88e-07	167

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	17.2735514018692	0.00483449420807607	0.0226721931116864
CHD2#1106	3	7.75801712558764	0.00335152246453634	0.0172905381680355
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418728780215783
FOS#2353	3	6.7484664816708	0.00503245277631794	0.0234541628589348
GTF2B#2959	2	15.9719149671621	0.00563658572353722	0.0254685202206673
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319935900267714
IRF3#3661	2	23.4909761057448	0.00264110142537554	0.0145920748963019
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0465953243153984
NANOG#79923	2	14.6223892405063	0.00669875771536376	0.0284811739551732
NFYA#4800	3	13.8191855248729	0.000613241180673451	0.00508424987444269
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.00618415752474559
NR2C2#7182	2	16.3073054526204	0.00541182534464822	0.0245517408961259
REST#5978	3	7.23752153709602	0.00410469730419261	0.0195713331698581
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.0123818799414392
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00794599164419831
STAT1#6772	3	15.5299406228994	0.00043408865517555	0.00404892248440468
STAT2#6773	2	32.6318855932203	0.00137958877512552	0.00898216271338034
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321355844552042
TFAP2A#7020	3	12.3889757797837	0.00084694130358843	0.00637963958207516
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0482797297416276
USF2#7392	3	9.7441480388022	0.00171834184841007	0.0107147832292137

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.