Coexpression cluster:C4278

Full id: C4278_liver_Monocytederived_hepatocellular_Macrophage_Hepatocyte_CD14_small

Phase1 CAGE Peaks

Hg19::chr3:126242976..126243008,+	p1@CHST13
Hg19::chr3:126243130..126243153,+	p2@CHST13
Hg19::chr3:126243162..126243176,+	p3@CHST13

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><br>

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Cell Type

Ontology term	p-value	n
myeloid leukocyte	5.17e-46	72
granulocyte monocyte progenitor cell	3.72e-41	67
myeloid lineage restricted progenitor cell	3.75e-40	66
monopoietic cell	2.32e-39	59
monocyte	2.32e-39	59
monoblast	2.32e-39	59
promonocyte	2.32e-39	59
macrophage dendritic cell progenitor	2.04e-37	61
myeloid cell	3.21e-35	108
common myeloid progenitor	3.21e-35	108
defensive cell	1.49e-33	48
phagocyte	1.49e-33	48
classical monocyte	6.70e-27	42
CD14-positive, CD16-negative classical monocyte	6.70e-27	42
hematopoietic stem cell	1.91e-19	168
angioblastic mesenchymal cell	1.91e-19	168
hematopoietic cell	2.78e-19	177
leukocyte	4.73e-19	136
hematopoietic oligopotent progenitor cell	4.57e-18	161
hematopoietic multipotent progenitor cell	4.57e-18	161
nongranular leukocyte	2.86e-16	115
hematopoietic lineage restricted progenitor cell	6.84e-16	120
stuff accumulating cell	1.23e-13	87
intermediate monocyte	2.11e-09	9
CD14-positive, CD16-positive monocyte	2.11e-09	9
macrophage	1.86e-08	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	9.03e-47	98
blood island	9.03e-47	98
hemolymphoid system	7.49e-41	108
bone marrow	1.71e-35	76
bone element	8.74e-35	82
skeletal element	1.07e-29	90
immune system	3.21e-29	93
skeletal system	1.52e-24	100
blood	1.36e-13	15
haemolymphatic fluid	1.36e-13	15
organism substance	1.36e-13	15
lateral plate mesoderm	3.98e-11	203
musculoskeletal system	1.92e-08	167
larynx	2.37e-07	9

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280391669292368
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326518437970785
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154525898690717
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123110983308667
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.0007586996395356
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247211765485816

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.