Coexpression cluster:C2117

Full id: C2117_immature_CD14_Basophils_Peripheral_Neutrophils_Mast_CD19

Phase1 CAGE Peaks

Hg19::chr11:18656354..18656376,-	p4@SPTY2D1
Hg19::chr13:41593392..41593403,-	p7@ELF1
Hg19::chr13:41593405..41593416,-	p9@ELF1
Hg19::chr3:41279208..41279212,+	p@chr3:41279208..41279212 +

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0050858	negative regulation of antigen receptor-mediated signaling pathway	0.00304662663369834
GO:0050860	negative regulation of T cell receptor signaling pathway	0.00304662663369834
GO:0050856	regulation of T cell receptor signaling pathway	0.00406216884493112
GO:0050854	regulation of antigen receptor-mediated signaling pathway	0.0050777110561639
GO:0050852	T cell receptor signaling pathway	0.00670257859413634
GO:0050851	antigen receptor-mediated signaling pathway	0.00670257859413634
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.00670257859413634
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.00670257859413634
GO:0002757	immune response-activating signal transduction	0.00670257859413634
GO:0002764	immune response-regulating signal transduction	0.00670257859413634
GO:0001817	regulation of cytokine production	0.00757040557464436
GO:0002253	activation of immune response	0.0120172494995879
GO:0050778	positive regulation of immune response	0.0124766614522884
GO:0002684	positive regulation of immune system process	0.0124766614522884
GO:0050776	regulation of immune response	0.0125449331975814
GO:0002682	regulation of immune system process	0.0125449331975814
GO:0051240	positive regulation of multicellular organismal process	0.0125449331975814
GO:0001816	cytokine production	0.0127506966521449
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0148589860380375
GO:0016564	transcription repressor activity	0.0215681822004676
GO:0045893	positive regulation of transcription, DNA-dependent	0.0215681822004676
GO:0051239	regulation of multicellular organismal process	0.0244576415871894
GO:0045941	positive regulation of transcription	0.0244576415871894
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0244576415871894
GO:0016563	transcription activator activity	0.0251042034616743
GO:0031325	positive regulation of cellular metabolic process	0.0285133005461511
GO:0009893	positive regulation of metabolic process	0.0294131114512605
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0306838825251047
GO:0006366	transcription from RNA polymerase II promoter	0.0448239320819985

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>disease_data<br>

---

Cell Type

Ontology term	p-value	n
hematopoietic stem cell	1.27e-63	172
angioblastic mesenchymal cell	1.27e-63	172
hematopoietic oligopotent progenitor cell	1.31e-60	165
hematopoietic multipotent progenitor cell	1.31e-60	165
hematopoietic cell	2.64e-58	182
leukocyte	8.17e-58	140
hematopoietic lineage restricted progenitor cell	2.72e-47	124
nongranular leukocyte	3.62e-46	119
myeloid cell	2.22e-44	112
common myeloid progenitor	2.22e-44	112
myeloid leukocyte	2.61e-38	76
granulocyte monocyte progenitor cell	9.16e-34	71
macrophage dendritic cell progenitor	5.43e-32	65
myeloid lineage restricted progenitor cell	5.81e-32	70
monopoietic cell	1.29e-30	63
monocyte	1.29e-30	63
monoblast	1.29e-30	63
promonocyte	1.29e-30	63
CD14-positive, CD16-negative classical monocyte	1.33e-27	42
classical monocyte	3.01e-26	45
mesenchymal cell	1.28e-16	358
connective tissue cell	2.86e-14	365
lymphocyte	8.54e-14	53
common lymphoid progenitor	8.54e-14	53
lymphoid lineage restricted progenitor cell	1.26e-13	52
motile cell	1.92e-13	390
lymphocyte of B lineage	9.96e-09	24
pro-B cell	9.96e-09	24
multi fate stem cell	2.93e-07	430
intermediate monocyte	7.62e-07	9
CD14-positive, CD16-positive monocyte	7.62e-07	9

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	5.21e-33	102
blood island	5.21e-33	102
bone element	2.42e-29	86
bone marrow	5.05e-29	80
hemolymphoid system	1.28e-28	112
skeletal element	7.17e-21	101
skeletal system	7.17e-21	101
immune system	4.35e-20	115
connective tissue	7.32e-14	375

Disease

Ontology term	p-value	n
hematologic cancer	7.69e-10	51
immune system cancer	7.69e-10	51
leukemia	2.84e-08	39
myeloid leukemia	9.89e-08	31

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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BATF#10538	2	12.1789008961518	0.00956675880504781	0.0360103338441717
BCL11A#53335	2	14.1847275518035	0.00710832858529874	0.0296113728658615
BCLAF1#9774	2	10.8263238050609	0.0120220381643258	0.0436385946004456
FOSL1#8061	2	19.8567898581865	0.00367705000923323	0.0185556351910664
IRF4#3662	2	10.9572563433721	0.0117453018068803	0.0428096452644928
JUNB#3726	2	15.3053163299106	0.00612694714847562	0.0270922661094731
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0386642090331216
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0465905848438806
MEF2C#4208	2	20.655677246312	0.00340257057944504	0.0173541567977077
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0482699604721534

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

---

This analysis result is provided for C0 - C305 clusters.