Coexpression cluster:C1390

Full id: C1390_Mast_CD8_Natural_Basophils_CD34_CD4_CD19

Phase1 CAGE Peaks

Hg19::chr14:23025207..23025219,-	p@chr14:23025207..23025219 -
Hg19::chr17:7743554..7743563,+	p@chr17:7743554..7743563 +
Hg19::chr1:67519625..67519640,-	p1@AB385301
Hg19::chr1:93812261..93812303,+	p2@DR1
Hg19::chr4:76598434..76598445,-	p6@G3BP2
Hg19::chr8:17780648..17780659,+	p4@PCM1

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:0007253	cytoplasmic sequestering of NF-kappaB	0.0120973193800372
GO:0042347	negative regulation of NF-kappaB import into nucleus	0.0120973193800372
GO:0000242	pericentriolar material	0.0120973193800372
GO:0042994	cytoplasmic sequestering of transcription factor	0.0120973193800372
GO:0051220	cytoplasmic sequestering of protein	0.0120973193800372
GO:0042308	negative regulation of protein import into nucleus	0.0120973193800372
GO:0042992	negative regulation of transcription factor import into nucleus	0.0120973193800372
GO:0042345	regulation of NF-kappaB import into nucleus	0.0120973193800372
GO:0042348	NF-kappaB import into nucleus	0.0120973193800372
GO:0046823	negative regulation of nucleocytoplasmic transport	0.0120973193800372
GO:0051224	negative regulation of protein transport	0.0120973193800372
GO:0030159	receptor signaling complex scaffold activity	0.0120973193800372
GO:0032947	protein complex scaffold	0.0120973193800372
GO:0042990	regulation of transcription factor import into nucleus	0.0120973193800372
GO:0042991	transcription factor import into nucleus	0.0120973193800372
GO:0033157	regulation of intracellular protein transport	0.0120973193800372
GO:0042306	regulation of protein import into nucleus	0.0120973193800372
GO:0044450	microtubule organizing center part	0.0120973193800372
GO:0032507	maintenance of cellular protein localization	0.0120973193800372
GO:0051651	maintenance of cellular localization	0.0120973193800372
GO:0032386	regulation of intracellular transport	0.0120973193800372
GO:0045185	maintenance of protein localization	0.0120973193800372
GO:0051223	regulation of protein transport	0.012367641059904
GO:0046822	regulation of nucleocytoplasmic transport	0.012367641059904
GO:0051051	negative regulation of transport	0.0126910111404423
GO:0048523	negative regulation of cellular process	0.0146464428917892
GO:0048519	negative regulation of biological process	0.0149820926239023
GO:0051235	maintenance of localization	0.0149820926239023
GO:0051028	mRNA transport	0.0284818448587953
GO:0050658	RNA transport	0.0284818448587953
GO:0051236	establishment of RNA localization	0.0284818448587953
GO:0050657	nucleic acid transport	0.0284818448587953
GO:0006403	RNA localization	0.0284818448587953
GO:0006606	protein import into nucleus	0.0286006223338466
GO:0051170	nuclear import	0.0286006223338466
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0295033620528052
GO:0003714	transcription corepressor activity	0.0295314200752571
GO:0051049	regulation of transport	0.0295578589690544
GO:0017038	protein import	0.0319304854904982
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.032108983109937
GO:0005813	centrosome	0.032108983109937
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0337643347359911
GO:0005815	microtubule organizing center	0.0348689724031423
GO:0006913	nucleocytoplasmic transport	0.0353498133259162
GO:0051169	nuclear transport	0.0353498133259162
GO:0045892	negative regulation of transcription, DNA-dependent	0.0449377503640029
GO:0005515	protein binding	0.0452836447329336
GO:0016564	transcription repressor activity	0.0452836447329336
GO:0006605	protein targeting	0.0452836447329336

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
hematopoietic stem cell	1.47e-29	168
angioblastic mesenchymal cell	1.47e-29	168
hematopoietic cell	7.74e-28	177
leukocyte	9.25e-28	136
hematopoietic oligopotent progenitor cell	6.55e-26	161
hematopoietic multipotent progenitor cell	6.55e-26	161
hematopoietic lineage restricted progenitor cell	3.96e-22	120
nongranular leukocyte	8.16e-21	115
mesenchymal cell	1.58e-13	354
lymphocyte	2.30e-13	53
common lymphoid progenitor	2.30e-13	53
connective tissue cell	4.93e-13	361
lymphoid lineage restricted progenitor cell	5.53e-13	52
nucleate cell	6.01e-13	55
myeloid cell	6.83e-13	108
common myeloid progenitor	6.83e-13	108
motile cell	9.39e-12	386
myeloid leukocyte	9.74e-11	72
granulocyte monocyte progenitor cell	5.11e-10	67
stem cell	8.73e-10	441
multi fate stem cell	2.68e-09	427
myeloid lineage restricted progenitor cell	5.27e-09	66
somatic stem cell	1.47e-08	433
T cell	4.63e-08	25
pro-T cell	4.63e-08	25
macrophage dendritic cell progenitor	4.76e-08	61
monopoietic cell	3.30e-07	59
monocyte	3.30e-07	59
monoblast	3.30e-07	59
promonocyte	3.30e-07	59

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.63e-15	98
blood island	2.63e-15	98
hemolymphoid system	2.80e-12	108
connective tissue	7.75e-12	371
blood	4.04e-09	15
haemolymphatic fluid	4.04e-09	15
organism substance	4.04e-09	15
bone marrow	7.29e-08	76
immune system	4.06e-07	93
bone element	6.83e-07	82
skeletal system	9.30e-07	100

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	11.5157009345794	0.0116272534680164	0.0424787044791744
GATA1#2623	3	6.78015407190022	0.00676576398334856	0.0287496795775466
GATA2#2624	3	6.372465866777	0.00805882130874255	0.0318881275541321
SP1#6667	4	3.7989209187606	0.0105224661679851	0.0389452067516547
SREBF1#6720	2	15.6686164801628	0.00641128316580946	0.0278902033719583
USF2#7392	3	6.4960986925348	0.00763431981530056	0.0314562167984446

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.