Coexpression cluster:C2054

Full id: C2054_Eosinophils_Dendritic_Neutrophils_CD19_CD14_Basophils_CD34

Phase1 CAGE Peaks

Hg19::chr10:30723045..30723060,+	p2@MAP3K8
Hg19::chr15:75495066..75495090,-	p@chr15:75495066..75495090 -
Hg19::chr19:45504688..45504782,+	p1@RELB
Hg19::chr6:44233297..44233330,-	p2@NFKBIE

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
0.000261809543829384	0.0331450882488	2	268	MAPK signaling pathway (KEGG):04010
4.24401547463794e-05	0.00895487265148605	2	108	T cell receptor signaling pathway (KEGG):04660
2.8113975272981e-07	0.00017796146347797	3	188	TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231
6.25100917324437e-05	0.00989222201665921	2	131	IL-5 up reg. targets (Netpath):NetPath_17
3.88503833680646e-06	0.00122961463359924	2	33	{NFKB1,33} (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:0043011	myeloid dendritic cell differentiation	0.0085925308502013
GO:0001773	myeloid dendritic cell activation	0.0085925308502013
GO:0045063	T-helper 1 cell differentiation	0.0085925308502013
GO:0042994	cytoplasmic sequestering of transcription factor	0.0085925308502013
GO:0002294	CD4-positive, alpha-beta T cell differentiation during immune response	0.0085925308502013
GO:0002292	T cell differentiation during immune response	0.0085925308502013
GO:0042093	T-helper cell differentiation	0.0085925308502013
GO:0002366	leukocyte activation during immune response	0.0085925308502013
GO:0002285	lymphocyte activation during immune response	0.0085925308502013
GO:0051220	cytoplasmic sequestering of protein	0.0085925308502013
GO:0002293	alpha-beta T cell differentiation during immune response	0.0085925308502013
GO:0002286	T cell activation during immune response	0.0085925308502013
GO:0002263	cell activation during immune response	0.0085925308502013
GO:0042308	negative regulation of protein import into nucleus	0.0085925308502013
GO:0042992	negative regulation of transcription factor import into nucleus	0.0085925308502013
GO:0043367	CD4-positive, alpha beta T cell differentiation	0.0085925308502013
GO:0042088	T-helper 1 type immune response	0.0085925308502013
GO:0046823	negative regulation of nucleocytoplasmic transport	0.0085925308502013
GO:0051224	negative regulation of protein transport	0.00881839046160363
GO:0046632	alpha-beta T cell differentiation	0.0103098228262197
GO:0004709	MAP kinase kinase kinase activity	0.0109026941205202
GO:0046631	alpha-beta T cell activation	0.0109026941205202
GO:0042990	regulation of transcription factor import into nucleus	0.0109026941205202
GO:0042991	transcription factor import into nucleus	0.0109026941205202
GO:0042306	regulation of protein import into nucleus	0.0109026941205202
GO:0033157	regulation of intracellular protein transport	0.0109026941205202
GO:0032507	maintenance of cellular protein localization	0.0111067793515641
GO:0051651	maintenance of cellular localization	0.0111067793515641
GO:0032386	regulation of intracellular transport	0.0111067793515641
GO:0045185	maintenance of protein localization	0.0111656867381263
GO:0002274	myeloid leukocyte activation	0.0112207691804314
GO:0051223	regulation of protein transport	0.0112723852677017
GO:0046822	regulation of nucleocytoplasmic transport	0.0113208501237992
GO:0002573	myeloid leukocyte differentiation	0.0113664417991907
GO:0051051	negative regulation of transport	0.0114094065671464
GO:0030217	T cell differentiation	0.0142699894330178
GO:0051235	maintenance of localization	0.0142699894330178
GO:0030098	lymphocyte differentiation	0.0216742314407406
GO:0002250	adaptive immune response	0.0235842708301034
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0235842708301034
GO:0030099	myeloid cell differentiation	0.0235842708301034
GO:0004702	receptor signaling protein serine/threonine kinase activity	0.0235842708301034
GO:0002521	leukocyte differentiation	0.0269146502620051
GO:0006606	protein import into nucleus	0.0273892766352992
GO:0051170	nuclear import	0.0273892766352992
GO:0042110	T cell activation	0.0273892766352992
GO:0003714	transcription corepressor activity	0.0292605890034004
GO:0051049	regulation of transport	0.0294516884986195
GO:0017038	protein import	0.0319866615733457
GO:0006913	nucleocytoplasmic transport	0.0385026978699054
GO:0046649	lymphocyte activation	0.0385026978699054
GO:0051169	nuclear transport	0.0385026978699054
GO:0030097	hemopoiesis	0.0389812617561175
GO:0048534	hemopoietic or lymphoid organ development	0.0409480756328063
GO:0005057	receptor signaling protein activity	0.0409480756328063
GO:0045321	leukocyte activation	0.0409480756328063
GO:0002520	immune system development	0.0409480756328063
GO:0001775	cell activation	0.0461752674458715
GO:0016564	transcription repressor activity	0.0464717294069291
GO:0006605	protein targeting	0.0465458612671562

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	3.58e-52	136
hematopoietic cell	2.36e-45	177
hematopoietic stem cell	8.71e-45	168
angioblastic mesenchymal cell	8.71e-45	168
nongranular leukocyte	1.39e-42	115
hematopoietic oligopotent progenitor cell	2.79e-42	161
hematopoietic multipotent progenitor cell	2.79e-42	161
hematopoietic lineage restricted progenitor cell	3.72e-40	120
myeloid leukocyte	1.34e-32	72
granulocyte monocyte progenitor cell	3.44e-29	67
macrophage dendritic cell progenitor	2.19e-28	61
defensive cell	2.30e-27	48
phagocyte	2.30e-27	48
monopoietic cell	4.37e-27	59
monocyte	4.37e-27	59
monoblast	4.37e-27	59
promonocyte	4.37e-27	59
myeloid cell	9.49e-27	108
common myeloid progenitor	9.49e-27	108
myeloid lineage restricted progenitor cell	3.83e-25	66
classical monocyte	5.13e-25	42
CD14-positive, CD16-negative classical monocyte	5.13e-25	42
lymphocyte	7.28e-14	53
common lymphoid progenitor	7.28e-14	53
lymphoid lineage restricted progenitor cell	1.99e-13	52
nucleate cell	2.67e-12	55
stuff accumulating cell	7.30e-11	87
mesenchymal cell	8.90e-11	354
connective tissue cell	1.62e-10	361
lymphocyte of B lineage	3.14e-10	24
pro-B cell	3.14e-10	24
dendritic cell	2.18e-07	10
stem cell	4.91e-07	441

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.13e-34	108
hematopoietic system	1.16e-33	98
blood island	1.16e-33	98
immune system	2.55e-28	93
bone marrow	2.58e-25	76
bone element	1.12e-22	82
skeletal element	3.53e-20	90
skeletal system	2.78e-16	100
lateral plate mesoderm	1.31e-15	203
connective tissue	9.21e-10	371
blood	4.04e-07	15
haemolymphatic fluid	4.04e-07	15
organism substance	4.04e-07	15

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
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00511080484559967
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00766293572793318
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.0044292989884729
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.0079392695845006
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321072015804117
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342174404712686

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.