Coexpression cluster:C3497

Full id: C3497_skeletal_CD14_Dendritic_Monocytederived_Basophils_Macrophage_immature

Phase1 CAGE Peaks

Hg19::chr15:51058130..51058152,-	p2@SPPL2A
Hg19::chr8:74888516..74888527,+	p3@TMEM70
Hg19::chr8:74888542..74888594,+	p2@TMEM70

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:0004190	aspartic-type endopeptidase activity	0.0449814078230606

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
granulocyte monocyte progenitor cell	5.74e-32	67
myeloid leukocyte	5.54e-31	72
macrophage dendritic cell progenitor	2.42e-29	61
myeloid lineage restricted progenitor cell	6.63e-29	66
monopoietic cell	4.46e-28	59
monocyte	4.46e-28	59
monoblast	4.46e-28	59
promonocyte	4.46e-28	59
defensive cell	1.35e-27	48
phagocyte	1.35e-27	48
classical monocyte	5.50e-26	42
CD14-positive, CD16-negative classical monocyte	5.50e-26	42
leukocyte	2.24e-20	136
hematopoietic lineage restricted progenitor cell	1.79e-18	120
myeloid cell	1.99e-18	108
common myeloid progenitor	1.99e-18	108
nongranular leukocyte	8.65e-17	115
stuff accumulating cell	7.65e-15	87
hematopoietic stem cell	1.31e-14	168
angioblastic mesenchymal cell	1.31e-14	168
mesenchymal cell	2.84e-14	354
hematopoietic cell	1.18e-13	177
hematopoietic oligopotent progenitor cell	4.67e-13	161
hematopoietic multipotent progenitor cell	4.67e-13	161
connective tissue cell	5.06e-13	361
motile cell	7.51e-11	386
multi fate stem cell	4.72e-10	427
somatic stem cell	1.39e-08	433
stem cell	5.96e-08	441

Uber Anatomy

Ontology term	p-value	n
bone marrow	1.37e-27	76
bone element	1.26e-25	82
hematopoietic system	1.69e-24	98
blood island	1.69e-24	98
immune system	2.08e-23	93
hemolymphoid system	2.82e-22	108
skeletal element	1.29e-19	90
skeletal system	1.43e-17	100
adult organism	2.82e-14	114
connective tissue	6.98e-13	371
lateral plate mesoderm	1.70e-10	203
musculoskeletal system	8.77e-10	167
mesoderm	2.33e-08	315
mesoderm-derived structure	2.33e-08	315
presumptive mesoderm	2.33e-08	315
tissue	1.50e-07	773

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
BCLAF1#9774	2	14.4350984067479	0.00620114743554613	0.0273797935664582
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189670857043638
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324539756383258
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461222350555197
PBX3#5090	2	14.6096751244961	0.00605612247321789	0.0268199709528221
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276035665894034
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.006287155191982

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.