Coexpression cluster:C1989

Full id: C1989_CD14_Hepatocyte_Peripheral_Basophils_Mast_dura_liver

Phase1 CAGE Peaks

Hg19::chr7:151554211..151554214,-	p@chr7:151554211..151554214 -
Hg19::chr7:151574171..151574187,-	p19@PRKAG2
Hg19::chr7:151574191..151574215,-	p4@PRKAG2
Hg19::chr7:151574231..151574246,-	p12@PRKAG2
Hg19::chr7:151574445..151574459,-	p10@PRKAG2

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
leukocyte	1.46e-38	140
myeloid leukocyte	1.91e-33	76
nongranular leukocyte	1.05e-32	119
granulocyte monocyte progenitor cell	5.43e-32	71
hematopoietic lineage restricted progenitor cell	3.02e-31	124
macrophage dendritic cell progenitor	3.69e-31	65
hematopoietic stem cell	1.10e-30	172
angioblastic mesenchymal cell	1.10e-30	172
monopoietic cell	2.24e-30	63
monocyte	2.24e-30	63
monoblast	2.24e-30	63
promonocyte	2.24e-30	63
CD14-positive, CD16-negative classical monocyte	5.91e-30	42
myeloid lineage restricted progenitor cell	3.83e-29	70
hematopoietic oligopotent progenitor cell	1.18e-28	165
hematopoietic multipotent progenitor cell	1.18e-28	165
hematopoietic cell	3.10e-28	182
classical monocyte	9.81e-28	45
myeloid cell	1.84e-24	112
common myeloid progenitor	1.84e-24	112
mature alpha-beta T cell	1.23e-07	18
alpha-beta T cell	1.23e-07	18
immature T cell	1.23e-07	18
mature T cell	1.23e-07	18
immature alpha-beta T cell	1.23e-07	18
intermediate monocyte	2.50e-07	9
CD14-positive, CD16-positive monocyte	2.50e-07	9

Uber Anatomy

Ontology term	p-value	n
adult organism	6.51e-33	115
hematopoietic system	1.68e-31	102
blood island	1.68e-31	102
hemolymphoid system	2.67e-27	112
bone marrow	1.15e-25	80
bone element	2.79e-24	86
skeletal element	4.14e-18	101
skeletal system	4.14e-18	101
immune system	5.82e-17	115
neural tube	3.14e-09	57
neural rod	3.14e-09	57
future spinal cord	3.14e-09	57
neural keel	3.14e-09	57
anterior neural tube	5.72e-08	42
regional part of forebrain	9.30e-08	41
forebrain	9.30e-08	41
future forebrain	9.30e-08	41
regional part of brain	2.33e-07	59
regional part of cerebral cortex	2.74e-07	22
blood	4.60e-07	15
haemolymphatic fluid	4.60e-07	15
organism substance	4.60e-07	15
telencephalon	5.70e-07	34

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	4	4.28820509846002	0.00515201558824328	0.0239451451212914
E2F1#1869	4	3.92591137190346	0.00721498454710636	0.0298840282020718
E2F6#1876	4	4.01372458535791	0.00663211823393388	0.0283050057714773
ELF1#1997	4	3.40647836704603	0.0123506610529955	0.0447428176389675
ESR1#2099	4	24.6148826369236	5.42856809638808e-06	0.000165630798544749
MYC#4609	4	4.17782549728752	0.00569196903682344	0.0256920889548277
SMARCB1#6598	4	14.6021726249259	4.30486693344344e-05	0.000768803005577803

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.