Coexpression cluster:C3145

Full id: C3145_Neutrophils_left_CD14_heart_Eosinophils_breast_mature

Phase1 CAGE Peaks

Hg19::chr11:33278811..33279020,+	p1@HIPK3
Hg19::chr11:33279850..33279931,+	p2@HIPK3
Hg19::chr4:15656923..15657009,-	p1@FBXL5

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:0043508	negative regulation of JNK activity	0.00571041708603294
GO:0018107	peptidyl-threonine phosphorylation	0.00571041708603294
GO:0018210	peptidyl-threonine modification	0.00571041708603294
GO:0018209	peptidyl-serine modification	0.0114196574596843
GO:0018105	peptidyl-serine phosphorylation	0.0114196574596843
GO:0043407	negative regulation of MAP kinase activity	0.020387742737772
GO:0043506	regulation of JNK activity	0.020387742737772
GO:0006469	negative regulation of protein kinase activity	0.0330794695081121
GO:0033673	negative regulation of kinase activity	0.0330794695081121
GO:0051348	negative regulation of transferase activity	0.0330794695081121
GO:0016567	protein ubiquitination	0.0330794695081121
GO:0043687	post-translational protein modification	0.0330794695081121
GO:0032446	protein modification by small protein conjugation	0.0330794695081121
GO:0000151	ubiquitin ligase complex	0.0330794695081121
GO:0043086	negative regulation of catalytic activity	0.0330794695081121
GO:0043405	regulation of MAP kinase activity	0.0331478301936655
GO:0006464	protein modification process	0.0361365010347462
GO:0043412	biopolymer modification	0.0363031783622391
GO:0018193	peptidyl-amino acid modification	0.0363031783622391
GO:0004842	ubiquitin-protein ligase activity	0.044017486364433
GO:0008639	small protein conjugating enzyme activity	0.044017486364433
GO:0006916	anti-apoptosis	0.044017486364433

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	8.58e-32	72
granulocyte monocyte progenitor cell	2.10e-28	67
macrophage dendritic cell progenitor	1.21e-26	61
monopoietic cell	5.78e-26	59
monocyte	5.78e-26	59
monoblast	5.78e-26	59
promonocyte	5.78e-26	59
defensive cell	1.81e-25	48
phagocyte	1.81e-25	48
classical monocyte	3.20e-25	42
CD14-positive, CD16-negative classical monocyte	3.20e-25	42
myeloid lineage restricted progenitor cell	4.26e-25	66
leukocyte	1.25e-21	136
hematopoietic lineage restricted progenitor cell	9.12e-18	120
nongranular leukocyte	3.07e-17	115
myeloid cell	6.67e-17	108
common myeloid progenitor	6.67e-17	108
hematopoietic stem cell	7.29e-14	168
angioblastic mesenchymal cell	7.29e-14	168
hematopoietic oligopotent progenitor cell	2.98e-13	161
hematopoietic multipotent progenitor cell	2.98e-13	161
stuff accumulating cell	6.07e-12	87
hematopoietic cell	8.17e-12	177

Uber Anatomy

Ontology term	p-value	n
adult organism	1.18e-40	114
hematopoietic system	7.26e-28	98
blood island	7.26e-28	98
hemolymphoid system	3.96e-25	108
bone marrow	1.34e-23	76
immune system	1.40e-20	93
bone element	1.59e-20	82
skeletal element	5.49e-20	90
skeletal system	1.39e-17	100
neural tube	3.09e-11	56
neural rod	3.09e-11	56
future spinal cord	3.09e-11	56
neural keel	3.09e-11	56
regional part of nervous system	3.36e-10	53
regional part of brain	3.36e-10	53
regional part of forebrain	1.20e-09	41
forebrain	1.20e-09	41
anterior neural tube	1.20e-09	41
future forebrain	1.20e-09	41
central nervous system	4.10e-08	81
brain	5.26e-08	68
future brain	5.26e-08	68
musculoskeletal system	6.34e-08	167
brain grey matter	1.37e-07	34
gray matter	1.37e-07	34
telencephalon	2.74e-07	34
nervous system	4.76e-07	89
regional part of telencephalon	6.83e-07	32

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189216262437891
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323731260507157
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319139603481961
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108343351877342
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172341275810465
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247409206956484
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328031386531892

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.