Coexpression cluster:C995

Full id: C995_B_plasma_lymphoma_xeroderma_acute_Burkitt_b

Phase1 CAGE Peaks

Hg19::chr11:60233507..60233518,+	p3@MS4A1
Hg19::chr1:207103754..207103765,-	p12@PIGR
Hg19::chr3:105975093..105975118,+	p@chr3:105975093..105975118 +
Hg19::chr3:186739681..186739693,+	p7@ST6GAL1
Hg19::chr3:186739710..186739719,+	p14@ST6GAL1
Hg19::chr3:186739722..186739731,+	p13@ST6GAL1
Hg19::chr8:110535027..110535055,+	p2@PKHD1L1
Hg19::chr8:110535062..110535067,+	p4@PKHD1L1

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:0003835	beta-galactoside alpha-2,6-sialyltransferase activity	0.0268432668755767
GO:0009311	oligosaccharide metabolic process	0.0408673311549087
GO:0008373	sialyltransferase activity	0.0408673311549087
GO:0006955	immune response	0.0408673311549087
GO:0005887	integral to plasma membrane	0.0408673311549087
GO:0031226	intrinsic to plasma membrane	0.0408673311549087
GO:0002376	immune system process	0.0408673311549087
GO:0009306	protein secretion	0.0408673311549087
GO:0030173	integral to Golgi membrane	0.0408673311549087
GO:0042113	B cell activation	0.0408673311549087
GO:0031228	intrinsic to Golgi membrane	0.0418550013339888
GO:0006959	humoral immune response	0.0418550013339888
GO:0016021	integral to membrane	0.0422278845053486
GO:0031224	intrinsic to membrane	0.0422278845053486
GO:0044425	membrane part	0.048599195518169
GO:0031301	integral to organelle membrane	0.048599195518169
GO:0044459	plasma membrane part	0.048599195518169
GO:0031300	intrinsic to organelle membrane	0.048599195518169
GO:0008565	protein transporter activity	0.048599195518169
GO:0046649	lymphocyte activation	0.048599195518169
GO:0006486	protein amino acid glycosylation	0.048599195518169
GO:0005057	receptor signaling protein activity	0.048599195518169
GO:0043413	biopolymer glycosylation	0.048599195518169
GO:0045321	leukocyte activation	0.048599195518169
GO:0009101	glycoprotein biosynthetic process	0.048599195518169

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
lymphocyte of B lineage	1.21e-27	24
pro-B cell	1.21e-27	24
B cell	2.36e-16	14
nongranular leukocyte	3.63e-12	119
lymphocyte	9.90e-12	53
common lymphoid progenitor	9.90e-12	53
lymphoid lineage restricted progenitor cell	5.76e-11	52
leukocyte	9.08e-11	140
hematopoietic lineage restricted progenitor cell	1.38e-09	124
hematopoietic stem cell	2.15e-09	172
angioblastic mesenchymal cell	2.15e-09	172
hematopoietic oligopotent progenitor cell	2.19e-08	165
hematopoietic multipotent progenitor cell	2.19e-08	165
hematopoietic cell	6.29e-08	182

Uber Anatomy

Ontology term	p-value	n
adult organism	2.19e-49	115
neural tube	3.05e-12	57
neural rod	3.05e-12	57
future spinal cord	3.05e-12	57
neural keel	3.05e-12	57
regional part of forebrain	3.25e-11	41
forebrain	3.25e-11	41
future forebrain	3.25e-11	41
anterior neural tube	9.36e-11	42
blood	9.89e-10	15
haemolymphatic fluid	9.89e-10	15
organism substance	9.89e-10	15
regional part of brain	1.09e-09	59
telencephalon	2.49e-09	34
gray matter	5.43e-09	34
brain grey matter	5.43e-09	34
regional part of telencephalon	8.88e-09	33
cerebral hemisphere	3.54e-08	32
brain	4.41e-08	69
future brain	4.41e-08	69
central nervous system	4.47e-08	82
nucleus of brain	1.90e-07	9
neural nucleus	1.90e-07	9
neural plate	3.18e-07	86
presumptive neural plate	3.18e-07	86

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
EBF1#1879	5	5.56654177910563	0.000744581328255861	0.00586406223827116
NFE2#4778	2	19.3010651629073	0.00445838869279524	0.0210988108517306
NFKB1#4790	7	4.80205549616961	4.48248622098168e-05	0.000794006747681658
PAX5#5079	7	5.8358698397806	1.18321811145587e-05	0.000299283401168177
POU2F2#5452	7	7.96785855052471	1.39153702916505e-06	5.41470699660838e-05
SPI1#6688	4	4.10216175426136	0.0102780066240076	0.0381933724890493
SRF#6722	4	6.8985891310839	0.00152207190456878	0.0097017801428904
TAF1#6872	6	2.50728471430897	0.0111173447561386	0.0408846920309293
TBP#6908	7	3.24342435120934	0.000635422362049205	0.005213928038188
ZEB1#6935	3	6.33316200657895	0.00927522268382487	0.0350417805627255

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.