Coexpression cluster:C2698

Full id: C2698_CD19_b_lymphoma_Burkitt_Dendritic_immature_Monocytederived

Phase1 CAGE Peaks

Hg19::chr2:33701352..33701361,+	p7@RASGRP3
Hg19::chr2:33701658..33701673,+	p2@RASGRP3
Hg19::chr2:33701684..33701702,+	p4@RASGRP3
Hg19::chr2:33701707..33701723,+	p1@RASGRP3

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

---

No GOStat results

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>

---

Cell Type

Ontology term	p-value	n
leukocyte	3.17e-29	140
hematopoietic lineage restricted progenitor cell	4.53e-27	124
nongranular leukocyte	5.53e-26	119
hematopoietic stem cell	2.74e-25	172
angioblastic mesenchymal cell	2.74e-25	172
hematopoietic oligopotent progenitor cell	1.52e-24	165
hematopoietic multipotent progenitor cell	1.52e-24	165
hematopoietic cell	2.37e-24	182
granulocyte monocyte progenitor cell	8.67e-15	71
myeloid lineage restricted progenitor cell	1.24e-14	70
myeloid leukocyte	1.58e-14	76
macrophage dendritic cell progenitor	2.17e-14	65
monopoietic cell	1.87e-13	63
monocyte	1.87e-13	63
monoblast	1.87e-13	63
promonocyte	1.87e-13	63
lymphocyte of B lineage	2.82e-13	24
pro-B cell	2.82e-13	24
myeloid cell	6.13e-13	112
common myeloid progenitor	6.13e-13	112
CD14-positive, CD16-negative classical monocyte	6.45e-13	42
lymphocyte	8.68e-12	53
common lymphoid progenitor	8.68e-12	53
lymphoid lineage restricted progenitor cell	1.73e-11	52
classical monocyte	1.53e-10	45
B cell	1.95e-08	14

Uber Anatomy

Ontology term	p-value	n
adult organism	3.30e-31	115
hemolymphoid system	1.43e-20	112
hematopoietic system	1.22e-19	102
blood island	1.22e-19	102
neural tube	4.13e-13	57
neural rod	4.13e-13	57
future spinal cord	4.13e-13	57
neural keel	4.13e-13	57
bone marrow	3.82e-12	80
immune system	5.78e-12	115
bone element	1.27e-10	86
regional part of brain	7.20e-10	59
anterior neural tube	8.66e-10	42
regional part of forebrain	1.49e-09	41
forebrain	1.49e-09	41
future forebrain	1.49e-09	41
telencephalon	1.76e-08	34
gray matter	1.82e-08	34
brain grey matter	1.82e-08	34
skeletal element	4.11e-08	101
skeletal system	4.11e-08	101
regional part of telencephalon	4.73e-08	33
central nervous system	6.05e-08	82
brain	6.64e-08	69
future brain	6.64e-08	69
neural plate	7.75e-08	86
presumptive neural plate	7.75e-08	86
blood	1.32e-07	15
haemolymphatic fluid	1.32e-07	15
organism substance	1.32e-07	15
cerebral hemisphere	1.93e-07	32
neurectoderm	4.08e-07	90
regional part of nervous system	5.26e-07	94
nervous system	5.26e-07	94

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
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0419051794107039
GATA2#2624	4	12.744931733554	3.78864877853583e-05	0.000722708109189961
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466396059255817
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00768595983875358
POU2F2#5452	3	6.82959304330689	0.00486047377520374	0.0227674480000226
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.0079740363205896
SMC3#9126	4	15.0449328449328	1.95092670935632e-05	0.000438838756404189
STAT2#6773	2	32.6318855932203	0.00137958877512552	0.00898552367230022
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322782548876772
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244658499977116
TCF12#6938	3	7.97584867663982	0.00309092039601307	0.0162855733649081
TCF7L2#6934	4	10.7701765631373	7.42969445082454e-05	0.00115606355594408
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0483221089777276

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.