Coexpression cluster:C2737

Full id: C2737_Monocytederived_granulocyte_chronic_Dendritic_Basophils_Macrophage_CD14

Phase1 CAGE Peaks

Hg19::chr3:196366555..196366572,+	p2@LRRC33
Hg19::chr3:196366587..196366604,+	p3@LRRC33
Hg19::chr3:196366616..196366690,+	p1@LRRC33 p2@PIGX
Hg19::chr3:196366873..196366890,-	p@chr3:196366873..196366890 -

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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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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	2.21e-77	168
angioblastic mesenchymal cell	2.21e-77	168
hematopoietic cell	7.46e-74	177
hematopoietic oligopotent progenitor cell	7.98e-73	161
hematopoietic multipotent progenitor cell	7.98e-73	161
leukocyte	1.22e-57	136
myeloid cell	2.38e-51	108
common myeloid progenitor	2.38e-51	108
hematopoietic lineage restricted progenitor cell	9.99e-50	120
nongranular leukocyte	4.77e-48	115
myeloid leukocyte	4.59e-32	72
granulocyte monocyte progenitor cell	1.67e-31	67
myeloid lineage restricted progenitor cell	1.98e-30	66
macrophage dendritic cell progenitor	1.09e-28	61
monopoietic cell	8.06e-28	59
monocyte	8.06e-28	59
monoblast	8.06e-28	59
promonocyte	8.06e-28	59
defensive cell	5.61e-24	48
phagocyte	5.61e-24	48
classical monocyte	4.52e-20	42
CD14-positive, CD16-negative classical monocyte	4.52e-20	42
nucleate cell	1.88e-18	55
lymphocyte	6.37e-18	53
common lymphoid progenitor	6.37e-18	53
lymphoid lineage restricted progenitor cell	2.41e-17	52
mesenchymal cell	3.14e-12	354
connective tissue cell	7.56e-11	361
stuff accumulating cell	1.57e-10	87
motile cell	1.08e-09	386
lymphocyte of B lineage	5.33e-09	24
pro-B cell	5.33e-09	24
T cell	8.95e-09	25
pro-T cell	8.95e-09	25
stem cell	1.34e-07	441
multi fate stem cell	2.70e-07	427
dendritic cell	4.15e-07	10

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	6.22e-36	98
blood island	6.22e-36	98
hemolymphoid system	3.83e-34	108
immune system	5.92e-28	93
bone marrow	8.43e-27	76
bone element	2.35e-22	82
skeletal element	2.52e-17	90
lateral plate mesoderm	2.50e-16	203
skeletal system	9.92e-14	100
connective tissue	8.43e-10	371
adult organism	2.93e-08	114
blood	5.79e-07	15
haemolymphatic fluid	5.79e-07	15
organism substance	5.79e-07	15

Disease

Ontology term	p-value	n
hematologic cancer	4.32e-21	51
immune system cancer	4.32e-21	51
leukemia	1.22e-20	39
myeloid leukemia	1.25e-16	31

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
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378753630297247
GATA1#2623	4	13.5603081438004	2.95627390049268e-05	0.000614917924504192
GATA2#2624	4	12.744931733554	3.78864877853583e-05	0.000723236501154275
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466411889683461
MEF2A#4205	3	14.057423182233	0.000583003885418661	0.00488905916085109
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00768801312395728
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00444534311756939
POU2F2#5452	3	6.82959304330689	0.00486047377520374	0.0227705118471495
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0483253720008202
USF2#7392	3	9.7441480388022	0.00171834184841007	0.010724387731929

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.