Coexpression cluster:C3185

Full id: C3185_chronic_acute_thymus_CD4_Hodgkin_CD8_NK

Phase1 CAGE Peaks

Hg19::chr11:6424016..6424033,-	p7@APBB1
Hg19::chr4:108969174..108969197,-	p@chr4:108969174..108969197 -
Hg19::chr7:142498763..142498785,+	p3@AJ568018

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:0050760	negative regulation of thymidylate synthase biosynthetic process	0.00237450449389693
GO:0050758	regulation of thymidylate synthase biosynthetic process	0.00237450449389693
GO:0050757	thymidylate synthase biosynthetic process	0.00237450449389693
GO:0045749	negative regulation of S phase of mitotic cell cycle	0.0123009907713758
GO:0001540	beta-amyloid binding	0.0123009907713758
GO:0007090	regulation of S phase of mitotic cell cycle	0.0123009907713758
GO:0045930	negative regulation of progression through mitotic cell cycle	0.0123009907713758
GO:0033261	regulation of progression through S phase	0.0123009907713758
GO:0000084	S phase of mitotic cell cycle	0.0123009907713758
GO:0030426	growth cone	0.0123009907713758
GO:0030427	site of polarized growth	0.0123009907713758
GO:0051320	S phase	0.0124624789486762
GO:0007346	regulation of progression through mitotic cell cycle	0.0175268017854181
GO:0030027	lamellipodium	0.0194594735801954
GO:0017148	negative regulation of translation	0.0194594735801954
GO:0031327	negative regulation of cellular biosynthetic process	0.0200219068535414
GO:0009890	negative regulation of biosynthetic process	0.0202299818924186
GO:0030308	negative regulation of cell growth	0.0202299818924186
GO:0045792	negative regulation of cell size	0.0202299818924186
GO:0045926	negative regulation of growth	0.0217075291219072
GO:0031252	leading edge	0.0243979520439284
GO:0051329	interphase of mitotic cell cycle	0.0274886381140926
GO:0051325	interphase	0.0275265936430817
GO:0009615	response to virus	0.0275265936430817
GO:0007050	cell cycle arrest	0.0275265936430817
GO:0051248	negative regulation of protein metabolic process	0.0275265936430817
GO:0048771	tissue remodeling	0.0275265936430817
GO:0007409	axonogenesis	0.0275265936430817
GO:0045087	innate immune response	0.0275265936430817
GO:0048667	neuron morphogenesis during differentiation	0.0275265936430817
GO:0048812	neurite morphogenesis	0.0275265936430817
GO:0000904	cellular morphogenesis during differentiation	0.0279972299614313
GO:0031175	neurite development	0.0290841708536053
GO:0048666	neuron development	0.0321926668132127
GO:0001558	regulation of cell growth	0.0327848518702859
GO:0006417	regulation of translation	0.0327848518702859
GO:0031326	regulation of cellular biosynthetic process	0.0327848518702859
GO:0016049	cell growth	0.0327848518702859
GO:0040008	regulation of growth	0.0327848518702859
GO:0032990	cell part morphogenesis	0.0327848518702859
GO:0030030	cell projection organization and biogenesis	0.0327848518702859
GO:0048858	cell projection morphogenesis	0.0327848518702859
GO:0008361	regulation of cell size	0.0327848518702859
GO:0051707	response to other organism	0.0327848518702859
GO:0030182	neuron differentiation	0.0327848518702859
GO:0032501	multicellular organismal process	0.0327848518702859
GO:0009889	regulation of biosynthetic process	0.0327848518702859
GO:0045786	negative regulation of progression through cell cycle	0.0332813801169429
GO:0048699	generation of neurons	0.0350566403475582
GO:0022008	neurogenesis	0.0371838177210064
GO:0009607	response to biotic stimulus	0.0396941228186807
GO:0006954	inflammatory response	0.0396941228186807
GO:0005125	cytokine activity	0.0411003848729342
GO:0042995	cell projection	0.0411003848729342
GO:0000278	mitotic cell cycle	0.0420210337736801
GO:0051704	multi-organism process	0.0421524736917254
GO:0000074	regulation of progression through cell cycle	0.0438597620073579
GO:0051726	regulation of cell cycle	0.0438597620073579
GO:0022403	cell cycle phase	0.044310832096655
GO:0031324	negative regulation of cellular metabolic process	0.0449813148471854
GO:0051246	regulation of protein metabolic process	0.0482182281231848
GO:0009611	response to wounding	0.0482182281231848
GO:0008134	transcription factor binding	0.0482182281231848
GO:0009892	negative regulation of metabolic process	0.0482182281231848

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
T cell	9.89e-46	25
pro-T cell	9.89e-46	25
lymphocyte	1.57e-40	53
common lymphoid progenitor	1.57e-40	53
mature alpha-beta T cell	7.67e-39	18
alpha-beta T cell	7.67e-39	18
immature T cell	7.67e-39	18
mature T cell	7.67e-39	18
immature alpha-beta T cell	7.67e-39	18
lymphoid lineage restricted progenitor cell	7.69e-39	52
nucleate cell	1.03e-38	55
CD8-positive, alpha-beta T cell	2.53e-22	11
nongranular leukocyte	9.18e-20	115
leukocyte	1.20e-18	136
CD4-positive, alpha-beta T cell	3.87e-16	6
hematopoietic stem cell	6.27e-15	168
angioblastic mesenchymal cell	6.27e-15	168
hematopoietic cell	1.67e-14	177
hematopoietic lineage restricted progenitor cell	7.89e-14	120
hematopoietic oligopotent progenitor cell	4.77e-12	161
hematopoietic multipotent progenitor cell	4.77e-12	161
naive T cell	9.29e-09	3
single nucleate cell	2.92e-08	3
mononuclear cell	2.92e-08	3
natural killer cell	9.23e-08	3
pro-NK cell	9.23e-08	3

Uber Anatomy

Ontology term	p-value	n
blood	1.11e-14	15
haemolymphatic fluid	1.11e-14	15
organism substance	1.11e-14	15
hemopoietic organ	1.36e-12	7
immune organ	1.36e-12	7
thymus	4.18e-11	4
hemolymphoid system gland	4.18e-11	4
thymic region	4.18e-11	4
pharyngeal gland	4.18e-11	4
thymus primordium	4.18e-11	4
entire pharyngeal arch endoderm	1.22e-07	11
early pharyngeal endoderm	1.22e-07	11
pharyngeal epithelium	2.26e-07	6

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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No analysis results for this cluster

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.