Coexpression cluster:C218

Full id: C218_tonsil_lymph_CD19_spleen_colon_appendix_salivary

Phase1 CAGE Peaks

Hg19::chr14:106330824..106330846,-	p1@IGHJ3
Hg19::chr14:106380481..106380483,-	p@chr14:106380481..106380483 -
Hg19::chr14:106453155..106453176,-	p1@IGHV1-2
Hg19::chr14:106471723..106471733,-	p1@IGHV1-3
Hg19::chr14:106494587..106494603,-	p1@IGHV2-5
Hg19::chr14:106512292..106512308,-	p1@IGHV3-6
Hg19::chr14:106518922..106518940,-	p1@IGHV3-7
Hg19::chr14:106539557..106539581,-	p1@IGHV1-8
Hg19::chr14:106586656..106586668,-	p1@IGHV3-13
Hg19::chr14:106668105..106668116,-	p1@IGHV3-20
Hg19::chr14:106692191..106692211,-	p1@IGHV3-21
Hg19::chr14:106725723..106725742,-	p1@IGHV3-23
Hg19::chr14:106733624..106733650,-	p1@IGHV1-24
Hg19::chr14:106746150..106746153,-	p1@IGHV3-25
Hg19::chr14:106845840..106845851,-	p1@IGHV3-35
Hg19::chr14:106967526..106967551,-	p1@IGHV1-46
Hg19::chr14:106994333..106994352,-	p1@IGHV3-48
Hg19::chr14:107013453..107013460,-	p2@IGHV3-49
Hg19::chr14:107013465..107013481,-	p1@IGHV3-49
Hg19::chr14:107035208..107035226,-	p1@IGHV5-51
Hg19::chr14:107035284..107035314,-	p2@IGHV5-51
Hg19::chr14:107078851..107078874,-	p1@IGHV1-58
Hg19::chr14:107083690..107083722,-	p1@IGHV4-59
Hg19::chr14:107099659..107099670,-	p1@IGHV3-62
Hg19::chr14:107179265..107179287,-	p1@IGHV2-70
Hg19::chr14:107183929..107183940,-	p1@IGHV3-71
Hg19::chr14:107199464..107199472,-	p1@IGHV3-72
Hg19::chr14:107211459..107211478,-	p1@IGHV3-73
Hg19::chr14:107259809..107259829,-	p1@uc001yta.1
Hg19::chr14:107281429..107281433,-	p1@IGHV4-80
Hg19::chr19:42381173..42381198,+	p2@CD79A
Hg19::chr22:17403095..17403096,-	p1@IGKV2OR22-3
Hg19::chr22:22516550..22516571,+	p1@IGLV4-60
Hg19::chr22:22677237..22677284,+	p1@AY998676
Hg19::chr22:22681656..22681657,+	p1@IGLV1-50
Hg19::chr22:22712089..22712103,+	p1@IGLV1-47
Hg19::chr22:22723969..22723985,+	p1@IGLV7-46
Hg19::chr22:22730353..22730360,+	p1@IGLV5-45
Hg19::chr22:22735194..22735208,+	p1@IGLV1-44
Hg19::chr22:22749343..22749360,+	p1@IGLV7-43
Hg19::chr22:22764088..22764105,+	p1@IGLV1-40
Hg19::chr22:22764110..22764121,+	p2@IGLV1-40
Hg19::chr22:22781853..22781858,+	p1@IGLV5-37
Hg19::chr22:22786288..22786295,+	p1@IGLV1-36
Hg19::chr22:22922260..22922267,+	p1@IGLV2-34
Hg19::chr22:23006897..23006908,+	p1@ENST00000385099
Hg19::chr22:23010756..23010763,+	p1@IGLV3-27
Hg19::chr22:23029172..23029186,+	p2@IGLV3-25
Hg19::chr22:23029188..23029205,+	p1@IGLV3-25
Hg19::chr22:23063100..23063117,+	p1@IGLV3-19
Hg19::chr22:23077065..23077071,+	p1@IGLV2-18
Hg19::chr22:23114284..23114291,+	p1@IGLV3-12
Hg19::chr22:23134974..23134990,+	p1@IGLV2-11
Hg19::chr22:23154239..23154246,+	p1@IGLV3-10
Hg19::chr22:23161576..23161592,+	p1@IGLV3-9
Hg19::chr22:23165272..23165278,+	p1@MIR650
Hg19::chr22:23222894..23222909,+	p1@IGLV3-1
Hg19::chr22:23227695..23227702,-	p@chr22:23227695..23227702 -
Hg19::chr22:23227835..23227842,+	p@chr22:23227835..23227842 +
Hg19::chr22:23237558..23237573,+	p@chr22:23237558..23237573 +
Hg19::chr2:114163945..114163953,+	p1@ENST00000453673
Hg19::chr2:89185050..89185069,+	p1@uc002stl.2
Hg19::chr2:89247338..89247342,-	p1@IGKV1-5
Hg19::chr2:89278535..89278547,-	p1@IGKV3-7
Hg19::chr2:89399845..89399854,-	p1@IGKV1-16
Hg19::chr2:89513402..89513412,-	p1@IGKV1-27
Hg19::chr2:89890533..89890539,+	p1@uc010yts.1
Hg19::chr2:95637982..95637984,-	p1@ENST00000429316

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
2.72719518243547e-17	8.63157275240828e-15	17	511	Signaling in Immune system (Reactome):REACT_6900
4.06974933269274e-28	2.57615132759451e-25	14	48	{FCGR2B,50} (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:0003823	antigen binding	4.21115196817957e-05
GO:0006955	immune response	5.67426408314668e-05
GO:0002376	immune system process	6.98965686274625e-05
GO:0019815	B cell receptor complex	0.00536865337511534
GO:0019814	immunoglobulin complex	0.00536865337511534
GO:0005771	multivesicular body	0.00596490702026829
GO:0050853	B cell receptor signaling pathway	0.0140557926159866
GO:0001772	immunological synapse	0.0178836616630865
GO:0042100	B cell proliferation	0.0178836616630865
GO:0050851	antigen receptor-mediated signaling pathway	0.0196590009575182
GO:0030183	B cell differentiation	0.0196590009575182
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0196590009575182
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0196590009575182
GO:0002757	immune response-activating signal transduction	0.0196590009575182
GO:0002764	immune response-regulating signal transduction	0.0196590009575182
GO:0045121	lipid raft	0.023659252672592
GO:0009897	external side of plasma membrane	0.023659252672592
GO:0005770	late endosome	0.023659252672592
GO:0032943	mononuclear cell proliferation	0.023659252672592
GO:0046651	lymphocyte proliferation	0.023659252672592
GO:0042113	B cell activation	0.0259246100408165
GO:0030098	lymphocyte differentiation	0.0259598057034707
GO:0002253	activation of immune response	0.0275385060338675
GO:0050778	positive regulation of immune response	0.0306676533211757
GO:0002684	positive regulation of immune system process	0.0306676533211757
GO:0002521	leukocyte differentiation	0.0308542166241833
GO:0050776	regulation of immune response	0.0318196556640933
GO:0002682	regulation of immune system process	0.0318196556640933
GO:0051240	positive regulation of multicellular organismal process	0.0322514226524992
GO:0043235	receptor complex	0.0326537506581756
GO:0009986	cell surface	0.0424455817755085
GO:0046649	lymphocyte activation	0.043050663867282
GO:0030097	hemopoiesis	0.0433505808108114
GO:0048534	hemopoietic or lymphoid organ development	0.0448795842241041
GO:0045321	leukocyte activation	0.0448795842241041
GO:0002520	immune system development	0.0448795842241041
GO:0005768	endosome	0.0462833074571253
GO:0001775	cell activation	0.0487668118354535

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	7.90e-36	140
hematopoietic stem cell	5.96e-35	172
angioblastic mesenchymal cell	5.96e-35	172
nongranular leukocyte	5.49e-32	119
hematopoietic oligopotent progenitor cell	1.76e-31	165
hematopoietic multipotent progenitor cell	1.76e-31	165
hematopoietic lineage restricted progenitor cell	7.40e-30	124
hematopoietic cell	8.04e-30	182
lymphocyte	9.14e-20	53
common lymphoid progenitor	9.14e-20	53
lymphoid lineage restricted progenitor cell	2.45e-19	52
lymphocyte of B lineage	1.69e-15	24
pro-B cell	1.69e-15	24
myeloid leukocyte	7.85e-15	76
CD14-positive, CD16-negative classical monocyte	1.74e-13	42
myeloid cell	3.69e-13	112
common myeloid progenitor	3.69e-13	112
classical monocyte	3.21e-12	45
myeloid lineage restricted progenitor cell	4.03e-12	70
granulocyte monocyte progenitor cell	1.38e-11	71
monopoietic cell	2.15e-11	63
monocyte	2.15e-11	63
monoblast	2.15e-11	63
promonocyte	2.15e-11	63
B cell	4.39e-11	14
macrophage dendritic cell progenitor	6.86e-11	65

Uber Anatomy

Ontology term	p-value	n
adult organism	2.40e-47	115
hematopoietic system	1.20e-16	102
blood island	1.20e-16	102
hemolymphoid system	2.41e-14	112
bone marrow	8.83e-10	80
immune system	3.13e-09	115
bone element	2.53e-08	86
neural tube	2.60e-08	57
neural rod	2.60e-08	57
future spinal cord	2.60e-08	57
neural keel	2.60e-08	57
anterior neural tube	4.63e-07	42

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
POU2F2#5452	18	2.41044460352008	0.000297931662909141	0.00307771364417089

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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