Coexpression cluster:C1325

Full id: C1325_CD19_cord_Eosinophils_b_B_Neutrophils_acute

Phase1 CAGE Peaks

Hg19::chr11:102188224..102188235,+	p3@BIRC3
Hg19::chr11:102188241..102188255,+	p2@BIRC3
Hg19::chr17:38020392..38020477,-	p1@IKZF3
Hg19::chr2:231090344..231090361,-	p3@SP110
Hg19::chr2:231090433..231090469,+	p1@SP140
Hg19::chr2:231090471..231090504,+	p2@SP140

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:0008270	zinc ion binding	0.0136564976516669
GO:0046914	transition metal ion binding	0.0136564976516669
GO:0005062	hematopoietin/interferon-class (D200-domain) cytokine receptor signal transducer activity	0.0136564976516669
GO:0005634	nucleus	0.021856297443892
GO:0043169	cation binding	0.021856297443892
GO:0046872	metal ion binding	0.021856297443892
GO:0043167	ion binding	0.021856297443892
GO:0003677	DNA binding	0.0396340780388288
GO:0043231	intracellular membrane-bound organelle	0.0396340780388288
GO:0043227	membrane-bound organelle	0.0396340780388288
GO:0007498	mesoderm development	0.0408971864373122

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>

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Cell Type

Ontology term	p-value	n
leukocyte	4.82e-76	136
nongranular leukocyte	1.79e-62	115
hematopoietic lineage restricted progenitor cell	2.51e-60	120
hematopoietic stem cell	1.53e-53	168
angioblastic mesenchymal cell	1.53e-53	168
hematopoietic cell	2.73e-52	177
hematopoietic oligopotent progenitor cell	1.32e-50	161
hematopoietic multipotent progenitor cell	1.32e-50	161
lymphocyte	3.03e-36	53
common lymphoid progenitor	3.03e-36	53
lymphoid lineage restricted progenitor cell	2.27e-35	52
nucleate cell	5.57e-34	55
myeloid leukocyte	1.21e-30	72
granulocyte monocyte progenitor cell	4.99e-25	67
defensive cell	7.20e-25	48
phagocyte	7.20e-25	48
macrophage dendritic cell progenitor	5.61e-24	61
myeloid lineage restricted progenitor cell	1.81e-23	66
classical monocyte	2.81e-23	42
CD14-positive, CD16-negative classical monocyte	2.81e-23	42
monopoietic cell	3.85e-23	59
monocyte	3.85e-23	59
monoblast	3.85e-23	59
promonocyte	3.85e-23	59
lymphocyte of B lineage	1.12e-18	24
pro-B cell	1.12e-18	24
myeloid cell	8.10e-18	108
common myeloid progenitor	8.10e-18	108
T cell	2.42e-15	25
pro-T cell	2.42e-15	25
mature alpha-beta T cell	2.20e-14	18
alpha-beta T cell	2.20e-14	18
immature T cell	2.20e-14	18
mature T cell	2.20e-14	18
immature alpha-beta T cell	2.20e-14	18
B cell	2.57e-11	14
CD8-positive, alpha-beta T cell	3.18e-09	11
granulocyte	2.33e-07	8
stuff accumulating cell	4.62e-07	87

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	5.31e-34	98
blood island	5.31e-34	98
hemolymphoid system	3.59e-30	108
immune system	4.72e-21	93
bone marrow	2.31e-20	76
bone element	5.60e-18	82
adult organism	1.86e-14	114
skeletal element	1.98e-14	90
skeletal system	1.88e-11	100
blood	1.97e-11	15
haemolymphatic fluid	1.97e-11	15
organism substance	1.97e-11	15
lateral plate mesoderm	8.66e-07	203

Disease

Ontology term	p-value	n
lymphoma	3.96e-07	10

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
BATF#10538	3	12.1789008961518	0.0012598148712534	0.00846079386141299
BCL11A#53335	3	14.1847275518035	0.000808083184942481	0.00616835256192134
BCLAF1#9774	3	10.8263238050609	0.00177235104699106	0.0108877460735663
EBF1#1879	5	7.42205570547417	9.7002838805275e-05	0.00137966491651697
ELF1#1997	6	4.25809795880754	0.000167722477628883	0.00205090362265343
FOXA1#3169	3	5.54070987469273	0.0119217877786028	0.0433741933327353
GATA1#2623	3	6.78015407190022	0.00676576398334856	0.0287450014098503
IRF4#3662	5	18.2620939056201	1.14070523243612e-06	4.65913624444255e-05
MEF2A#4205	3	9.37161545482203	0.00268739994710391	0.0147977731362675
NFKB1#4790	6	5.48806342419384	3.65870229532191e-05	0.000706827985610664
NRF1#4899	3	6.10513972385545	0.00909016207939674	0.0343998636644002
PAX5#5079	6	6.66956553117783	1.13557256338955e-05	0.000289758277419597
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0379902750423763
POU2F2#5452	6	9.10612405774252	1.75272139021506e-06	6.59648537919533e-05
RFX5#5993	5	10.0399256893292	2.19894173045095e-05	0.000482469065938165
SMC3#9126	3	7.52246642246642	0.00503954071682855	0.0234798622825151
SRF#6722	3	6.8985891310839	0.0064424516893037	0.0279989684981561
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00572510065676611
TBP#6908	5	3.08897557258032	0.00664544827578693	0.0282809980226931
TCF12#6938	3	5.31723245109321	0.01336734573386	0.0472396109057829
TCF7L2#6934	3	5.38508828156867	0.0129048877993104	0.0463997513296442
USF2#7392	4	8.66146492337973	0.000463535508143562	0.00426755861556818
YY1#7528	6	4.91117074985386	7.12445972864136e-05	0.00112346587588642

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.