Coexpression cluster:C1185

Full id: C1185_splenic_myeloma_lymphoma_immature_acute_CD19_Burkitt

Phase1 CAGE Peaks

Hg19::chr12:9885606..9885619,-	p4@CLECL1
Hg19::chr12:9885630..9885668,-	p2@CLECL1
Hg19::chr12:9885678..9885698,-	p3@CLECL1
Hg19::chr12:9885702..9885717,-	p5@CLECL1
Hg19::chr12:9885767..9885808,-	p1@CLECL1
Hg19::chr3:121796686..121796695,+	p6@CD86
Hg19::chr3:121796697..121796747,+	p2@CD86

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:0043016	regulation of lymphotoxin A biosynthetic process	0.00239759062769123
GO:0043017	positive regulation of lymphotoxin A biosynthetic process	0.00239759062769123
GO:0045630	positive regulation of T-helper 2 cell differentiation	0.00239759062769123
GO:0032641	lymphotoxin A production	0.00239759062769123
GO:0042109	lymphotoxin A biosynthetic process	0.00239759062769123
GO:0045404	positive regulation of interleukin-4 biosynthetic process	0.00239759062769123
GO:0042097	interleukin-4 biosynthetic process	0.00239759062769123
GO:0045402	regulation of interleukin-4 biosynthetic process	0.00239759062769123
GO:0045624	positive regulation of T-helper cell differentiation	0.00239759062769123
GO:0045628	regulation of T-helper 2 cell differentiation	0.00239759062769123
GO:0032633	interleukin-4 production	0.00239759062769123
GO:0045064	T-helper 2 cell differentiation	0.00274719882404461
GO:0045622	regulation of T-helper cell differentiation	0.00299672360703993
GO:0002285	lymphocyte activation during immune response	0.00299672360703993
GO:0002293	alpha-beta T cell differentiation during immune response	0.00299672360703993
GO:0002294	CD4-positive, alpha-beta T cell differentiation during immune response	0.00299672360703993
GO:0002292	T cell differentiation during immune response	0.00299672360703993
GO:0042093	T-helper cell differentiation	0.00299672360703993
GO:0002366	leukocyte activation during immune response	0.00299672360703993
GO:0042092	T-helper 2 type immune response	0.00299672360703993
GO:0002286	T cell activation during immune response	0.00299672360703993
GO:0002263	cell activation during immune response	0.00299672360703993
GO:0043367	CD4-positive, alpha beta T cell differentiation	0.0030216518232285
GO:0045086	positive regulation of interleukin-2 biosynthetic process	0.0030216518232285
GO:0045076	regulation of interleukin-2 biosynthetic process	0.00376697693989987
GO:0046632	alpha-beta T cell differentiation	0.00376697693989987
GO:0015026	coreceptor activity	0.00376697693989987
GO:0042094	interleukin-2 biosynthetic process	0.00376697693989987
GO:0046631	alpha-beta T cell activation	0.00431884315484041
GO:0032623	interleukin-2 production	0.00461420708182391
GO:0042108	positive regulation of cytokine biosynthetic process	0.00844316002446495
GO:0030217	T cell differentiation	0.00844316002446495
GO:0045727	positive regulation of translation	0.0105817211871921
GO:0042035	regulation of cytokine biosynthetic process	0.0112936105942213
GO:0031328	positive regulation of cellular biosynthetic process	0.0112936105942213
GO:0030098	lymphocyte differentiation	0.011711202345814
GO:0042089	cytokine biosynthetic process	0.0117875550671227
GO:0042107	cytokine metabolic process	0.0117875550671227
GO:0009891	positive regulation of biosynthetic process	0.0118227649235901
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0122089120025065
GO:0002250	adaptive immune response	0.0122089120025065
GO:0051247	positive regulation of protein metabolic process	0.0133278245401661
GO:0002521	leukocyte differentiation	0.0137826168697267
GO:0042110	T cell activation	0.0146649241795027
GO:0001816	cytokine production	0.0165301320416057
GO:0045595	regulation of cell differentiation	0.0205975954769105
GO:0046649	lymphocyte activation	0.021695778430325
GO:0030097	hemopoiesis	0.022064169935319
GO:0048534	hemopoietic or lymphoid organ development	0.0232207415463573
GO:0045321	leukocyte activation	0.0232685887144564
GO:0002520	immune system development	0.0232685887144564
GO:0006417	regulation of translation	0.0232685887144564
GO:0031326	regulation of cellular biosynthetic process	0.0246851982290708
GO:0001775	cell activation	0.0254417994942434
GO:0009889	regulation of biosynthetic process	0.0259323005627626
GO:0008284	positive regulation of cell proliferation	0.0272056617714807
GO:0050793	regulation of developmental process	0.0272056617714807
GO:0045941	positive regulation of transcription	0.031588023573144
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0321608772250949
GO:0016563	transcription activator activity	0.0338034384215129
GO:0005529	sugar binding	0.0373172139940967
GO:0031325	positive regulation of cellular metabolic process	0.0386095807151983
GO:0009893	positive regulation of metabolic process	0.0406876863975909
GO:0051246	regulation of protein metabolic process	0.0432075775958719
GO:0042127	regulation of cell proliferation	0.0472481184952243
GO:0030246	carbohydrate binding	0.0474188548497282

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
hematopoietic stem cell	2.02e-82	168
angioblastic mesenchymal cell	2.02e-82	168
hematopoietic cell	5.61e-81	177
hematopoietic oligopotent progenitor cell	1.29e-78	161
hematopoietic multipotent progenitor cell	1.29e-78	161
leukocyte	1.80e-66	136
hematopoietic lineage restricted progenitor cell	2.12e-58	120
nongranular leukocyte	4.05e-58	115
myeloid cell	8.37e-46	108
common myeloid progenitor	8.37e-46	108
granulocyte monocyte progenitor cell	2.86e-30	67
lymphocyte of B lineage	5.94e-30	24
pro-B cell	5.94e-30	24
macrophage dendritic cell progenitor	3.34e-28	61
lymphocyte	4.03e-28	53
common lymphoid progenitor	4.03e-28	53
myeloid lineage restricted progenitor cell	2.41e-27	66
lymphoid lineage restricted progenitor cell	7.34e-27	52
myeloid leukocyte	1.21e-26	72
nucleate cell	1.29e-26	55
monopoietic cell	6.34e-26	59
monocyte	6.34e-26	59
monoblast	6.34e-26	59
promonocyte	6.34e-26	59
defensive cell	2.12e-24	48
phagocyte	2.12e-24	48
classical monocyte	3.21e-22	42
CD14-positive, CD16-negative classical monocyte	3.21e-22	42
mesenchymal cell	3.77e-21	354
connective tissue cell	4.10e-20	361
B cell	1.09e-17	14
motile cell	1.66e-16	386
dendritic cell	4.48e-14	10
multi fate stem cell	3.28e-12	427
conventional dendritic cell	6.31e-12	8
somatic stem cell	1.24e-11	433
stem cell	6.85e-11	441
stuff accumulating cell	9.33e-09	87
immature conventional dendritic cell	1.12e-08	5
common dendritic progenitor	1.12e-08	5
CD8-positive, alpha-beta T cell	4.77e-08	11
Langerhans cell	1.42e-07	5

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.52e-38	98
blood island	4.52e-38	98
hemolymphoid system	1.18e-35	108
immune system	1.02e-27	93
bone marrow	1.50e-26	76
bone element	1.69e-23	82
skeletal element	4.35e-20	90
connective tissue	2.59e-19	371
skeletal system	1.23e-16	100
lateral plate mesoderm	2.06e-09	203
blood	6.08e-09	15
haemolymphatic fluid	6.08e-09	15
organism substance	6.08e-09	15

Disease

Ontology term	p-value	n
hematologic cancer	1.96e-18	51
immune system cancer	1.96e-18	51
leukemia	6.99e-14	39
myeloid leukemia	1.19e-13	31
lymphoma	2.10e-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	5	17.3984298516455	2.2818035468994e-06	8.13897816375092e-05
NFKB1#4790	7	5.48806342419384	6.66568321176054e-06	0.000194783796573324
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223350631960347
SPI1#6688	7	8.20432350852273	3.99342038048841e-07	1.93266372158401e-05

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.