Coexpression cluster:C1787

Full id: C1787_embryonic_Eosinophils_CD34_CD14_immature_Basophils_CD19

Phase1 CAGE Peaks

Hg19::chr17:4852857..4852892,+	p@chr17:4852857..4852892 +
Hg19::chr17:73257101..73257120,+	p@chr17:73257101..73257120 +
Hg19::chr5:176881716..176881752,+	p3@PRR7
Hg19::chr5:176881798..176881811,+	p5@PRR7
Hg19::chrX:153626083..153626119,+	p6@RPL10

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:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	0.0360591075002943
GO:0005830	cytosolic ribosome (sensu Eukaryota)	0.0360591075002943
GO:0015934	large ribosomal subunit	0.0360591075002943
GO:0044445	cytosolic part	0.0461556576003768
GO:0033279	ribosomal subunit	0.0461556576003768

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
leukocyte	2.59e-34	140
hematopoietic stem cell	6.44e-30	172
angioblastic mesenchymal cell	6.44e-30	172
hematopoietic cell	8.85e-30	182
nongranular leukocyte	1.68e-27	119
hematopoietic oligopotent progenitor cell	1.07e-26	165
hematopoietic multipotent progenitor cell	1.07e-26	165
hematopoietic lineage restricted progenitor cell	2.20e-26	124
CD14-positive, CD16-negative classical monocyte	2.46e-23	42
classical monocyte	2.38e-22	45
myeloid leukocyte	3.35e-18	76
granulocyte monocyte progenitor cell	4.53e-15	71
macrophage dendritic cell progenitor	2.66e-14	65
myeloid cell	6.66e-14	112
common myeloid progenitor	6.66e-14	112
monopoietic cell	2.86e-13	63
monocyte	2.86e-13	63
monoblast	2.86e-13	63
promonocyte	2.86e-13	63
lymphocyte	7.09e-13	53
common lymphoid progenitor	7.09e-13	53
myeloid lineage restricted progenitor cell	8.91e-13	70
lymphoid lineage restricted progenitor cell	9.90e-13	52
native cell	7.18e-07	722
T cell	9.53e-07	25
pro-T cell	9.53e-07	25

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	7.67e-17	102
blood island	7.67e-17	102
hemolymphoid system	9.38e-14	112
bone element	5.68e-13	86
bone marrow	3.42e-12	80
skeletal element	1.24e-08	101
skeletal system	1.24e-08	101
immune system	3.43e-08	115

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
BCL11A#53335	2	11.3477820414428	0.0115705693374132	0.0422878881239536
CTCFL#140690	3	11.8478846153846	0.00120177034853823	0.00815063922533828
ELF1#1997	4	3.40647836704603	0.0123506610529955	0.0447366104711197
ETS1#2113	3	5.8372565533214	0.00925327904563143	0.0349740594327845
GABPB1#2553	4	5.65414706894574	0.00177669650209667	0.0109086658425911
JUNB#3726	2	12.2442530639285	0.00999049059334596	0.0374702595374007
MEF2A#4205	3	11.2459385457864	0.00139936678741195	0.00910298772410566
NANOG#79923	2	11.6979113924051	0.0109116495195608	0.0402259712027325
NFKB1#4790	5	5.48806342419384	0.000200816284746232	0.00239090879646736
SMARCA4#6597	2	62.7063613231552	0.000401412085940533	0.00386637248395678
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135344538851826
TCF12#6938	4	8.50757192174914	0.000361421557849226	0.00361141466515646
TFAP2C#7022	3	6.48553716591613	0.00685895151794	0.0290605289079974
ZEB1#6935	3	10.1330592105263	0.00189555692435707	0.0111620472272738
ZNF143#7702	3	8.10052593133674	0.00362487051209098	0.018332180108095

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.