Coexpression cluster:C1347

Full id: C1347_testis_Neutrophils_Eosinophils_CD14_Basophils_blood_Whole

Phase1 CAGE Peaks

Hg19::chr11:64545206..64545220,-	p18@SF1
Hg19::chr11:64545222..64545241,-	p14@SF1
Hg19::chr1:21503755..21503801,-	p6@EIF4G3
Hg19::chr1:33430424..33430450,-	p3@RNF19B
Hg19::chr22:40440137..40440179,-	p2@BC038752
Hg19::chr2:176867534..176867553,-	p3@KIAA1715

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:0022618	protein-RNA complex assembly	0.010613566923
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.0157454819616763
GO:0048662	negative regulation of smooth muscle cell proliferation	0.0157454819616763
GO:0000389	nuclear mRNA 3'-splice site recognition	0.0157454819616763
GO:0000339	RNA cap binding	0.0176333824446613
GO:0016281	eukaryotic translation initiation factor 4F complex	0.0195865918599737
GO:0048660	regulation of smooth muscle cell proliferation	0.0195865918599737
GO:0006376	mRNA splice site selection	0.0195865918599737
GO:0048659	smooth muscle cell proliferation	0.0195865918599737
GO:0033002	muscle cell proliferation	0.0251760894769034
GO:0065003	macromolecular complex assembly	0.0280184993791957
GO:0022607	cellular component assembly	0.0290365082605116
GO:0000245	spliceosome assembly	0.0290365082605116
GO:0003723	RNA binding	0.0351989918807554
GO:0005515	protein binding	0.0351989918807554
GO:0006446	regulation of translational initiation	0.0439881637215268
GO:0000375	RNA splicing, via transesterification reactions	0.0462747063103437
GO:0000398	nuclear mRNA splicing, via spliceosome	0.0462747063103437
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0462747063103437

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
classical monocyte	3.48e-14	42
CD14-positive, CD16-negative classical monocyte	3.48e-14	42
myeloid leukocyte	2.39e-13	72
defensive cell	2.85e-11	48
phagocyte	2.85e-11	48
leukocyte	2.33e-09	136
myeloid lineage restricted progenitor cell	7.83e-09	66
monopoietic cell	1.20e-08	59
monocyte	1.20e-08	59
monoblast	1.20e-08	59
promonocyte	1.20e-08	59
granulocyte	2.10e-08	8
macrophage dendritic cell progenitor	5.87e-08	61
blood cell	6.17e-08	11
granulocyte monocyte progenitor cell	8.26e-08	67
myeloid cell	1.18e-07	108
common myeloid progenitor	1.18e-07	108
hematopoietic stem cell	8.26e-07	168
angioblastic mesenchymal cell	8.26e-07	168

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.56e-16	53
regional part of brain	1.56e-16	53
neural tube	2.29e-16	56
neural rod	2.29e-16	56
future spinal cord	2.29e-16	56
neural keel	2.29e-16	56
central nervous system	4.04e-15	81
brain	1.61e-14	68
future brain	1.61e-14	68
regional part of forebrain	4.66e-13	41
forebrain	4.66e-13	41
anterior neural tube	4.66e-13	41
future forebrain	4.66e-13	41
hematopoietic system	2.03e-12	98
blood island	2.03e-12	98
adult organism	3.86e-12	114
hemolymphoid system	1.13e-11	108
nervous system	1.30e-11	89
brain grey matter	1.42e-11	34
gray matter	1.42e-11	34
telencephalon	1.94e-11	34
neocortex	5.66e-11	20
cerebral hemisphere	7.30e-11	32
regional part of cerebral cortex	1.68e-10	22
regional part of telencephalon	1.94e-10	32
cerebral cortex	4.90e-10	25
pallium	4.90e-10	25
neural plate	6.83e-10	82
presumptive neural plate	6.83e-10	82
blood	7.54e-09	15
haemolymphatic fluid	7.54e-09	15
organism substance	7.54e-09	15
neurectoderm	1.13e-08	86
pre-chordal neural plate	2.00e-08	61
bone marrow	5.78e-07	76
immune system	9.53e-07	93
bone element	9.93e-07	82

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)
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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
NRF1#4899	3	6.10513972385545	0.00909016207939674	0.034401110171762
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0379970532102043
SIN3A#25942	4	3.60592315121009	0.0127389384448714	0.0459375040481983

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.