Coexpression cluster:C342

Full id: C342_xeroderma_b_B_splenic_plasma_Burkitt_thymus

Phase1 CAGE Peaks

Hg19::chr10:73976884..73976894,-	p5@ASCC1
Hg19::chr11:120484784..120484795,+	p@chr11:120484784..120484795 +
Hg19::chr12:111106975..111106991,-	p@chr12:111106975..111106991 -
Hg19::chr12:111107001..111107019,-	p@chr12:111107001..111107019 -
Hg19::chr14:21134939..21134952,-	p@chr14:21134939..21134952 -
Hg19::chr16:81844780..81844795,+	p@chr16:81844780..81844795 +
Hg19::chr16:81844812..81844828,+	p@chr16:81844812..81844828 +
Hg19::chr17:16875371..16875447,-	p1@TNFRSF13B
Hg19::chr17:28539815..28539831,-	p@chr17:28539815..28539831 -
Hg19::chr17:46189327..46189378,+	p4@SNX11
Hg19::chr17:46189383..46189391,+	p6@SNX11
Hg19::chr17:67513291..67513311,+	p@chr17:67513291..67513311 +
Hg19::chr18:60825483..60825499,-	p@chr18:60825483..60825499 -
Hg19::chr18:60984634..60984649,+	p@chr18:60984634..60984649 +
Hg19::chr19:14721826..14721829,+	p@chr19:14721826..14721829 +
Hg19::chr1:101838740..101838743,+	p@chr1:101838740..101838743 +
Hg19::chr1:160616804..160616822,-	p1@SLAMF1
Hg19::chr1:75198161..75198173,+	p@chr1:75198161..75198173 +
Hg19::chr21:26797217..26797228,-	p5@LINC00158
Hg19::chr21:26797257..26797267,-	p7@LINC00158
Hg19::chr22:39843128..39843135,+	p@chr22:39843128..39843135 +
Hg19::chr22:42834287..42834305,+	p2@ENST00000428765
Hg19::chr2:242052105..242052116,-	p12@PASK
Hg19::chr2:25585766..25585790,+	p@chr2:25585766..25585790 +
Hg19::chr2:45006189..45006201,+	p@chr2:45006189..45006201 +
Hg19::chr4:154410402..154410460,+	p@chr4:154410402..154410460 +
Hg19::chr5:96267483..96267496,+	p@chr5:96267483..96267496 +
Hg19::chr5:96267508..96267529,+	p@chr5:96267508..96267529 +
Hg19::chr7:44500049..44500072,-	p@chr7:44500049..44500072 -
Hg19::chr7:99809276..99809341,+	p2@STAG3
Hg19::chr8:22559141..22559159,-	p@chr8:22559141..22559159 -
Hg19::chr8:22576954..22576965,+	p@chr8:22576954..22576965 +
Hg19::chrX:12884985..12885009,+	p6@TLR7

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:0030889	negative regulation of B cell proliferation	0.0135934311345815
GO:0009986	cell surface	0.0135934311345815
GO:0035197	siRNA binding	0.0135934311345815
GO:0046649	lymphocyte activation	0.0135934311345815
GO:0045321	leukocyte activation	0.0135934311345815
GO:0001775	cell activation	0.0135934311345815
GO:0045359	positive regulation of interferon-beta biosynthetic process	0.0135934311345815
GO:0032608	interferon-beta production	0.0135934311345815
GO:0045357	regulation of interferon-beta biosynthetic process	0.0135934311345815
GO:0001782	B cell homeostasis	0.0135934311345815
GO:0045356	positive regulation of interferon-alpha biosynthetic process	0.0135934311345815
GO:0045350	interferon-beta biosynthetic process	0.0135934311345815
GO:0045354	regulation of interferon-alpha biosynthetic process	0.0135934311345815
GO:0032607	interferon-alpha production	0.0135934311345815
GO:0045349	interferon-alpha biosynthetic process	0.0135934311345815
GO:0050869	negative regulation of B cell activation	0.0135934311345815
GO:0045416	positive regulation of interleukin-8 biosynthetic process	0.0135934311345815
GO:0007130	synaptonemal complex assembly	0.0135934311345815
GO:0007129	synapsis	0.0144640387975788
GO:0032606	interferon type I production	0.0144640387975788
GO:0045414	regulation of interleukin-8 biosynthetic process	0.0144640387975788
GO:0045351	interferon type I biosynthetic process	0.0144640387975788
GO:0042228	interleukin-8 biosynthetic process	0.0144640387975788
GO:0045078	positive regulation of interferon-gamma biosynthetic process	0.0144640387975788
GO:0002260	lymphocyte homeostasis	0.0144640387975788
GO:0030888	regulation of B cell proliferation	0.0144640387975788
GO:0050794	regulation of cellular process	0.0144640387975788
GO:0002376	immune system process	0.0144640387975788
GO:0032637	interleukin-8 production	0.0144640387975788
GO:0050672	negative regulation of lymphocyte proliferation	0.0144640387975788
GO:0032945	negative regulation of mononuclear cell proliferation	0.0144640387975788
GO:0045072	regulation of interferon-gamma biosynthetic process	0.0152845094127478
GO:0000795	synaptonemal complex	0.0155828295736444
GO:0042095	interferon-gamma biosynthetic process	0.0155828295736444
GO:0001776	leukocyte homeostasis	0.0160671495404434
GO:0050789	regulation of biological process	0.0160671495404434
GO:0048872	homeostasis of number of cells	0.0165194171830189
GO:0051607	defense response to virus	0.0171554937858324
GO:0032609	interferon-gamma production	0.017565387589091
GO:0042100	B cell proliferation	0.017565387589091
GO:0004871	signal transducer activity	0.017565387589091
GO:0060089	molecular transducer activity	0.017565387589091
GO:0042127	regulation of cell proliferation	0.017565387589091
GO:0051250	negative regulation of lymphocyte activation	0.0175894684695822
GO:0003727	single-stranded RNA binding	0.0181021819400095
GO:0065007	biological regulation	0.0192416850047778
GO:0050864	regulation of B cell activation	0.0216552828916914
GO:0000794	condensed nuclear chromosome	0.0262791975789329
GO:0007127	meiosis I	0.0273988804587277
GO:0042108	positive regulation of cytokine biosynthetic process	0.0328333983870052
GO:0050670	regulation of lymphocyte proliferation	0.0328333983870052
GO:0032944	regulation of mononuclear cell proliferation	0.0328333983870052
GO:0008283	cell proliferation	0.0350210979489749
GO:0009897	external side of plasma membrane	0.0364814455963035
GO:0000793	condensed chromosome	0.0364814455963035
GO:0032943	mononuclear cell proliferation	0.0364814455963035
GO:0045727	positive regulation of translation	0.0364814455963035
GO:0046651	lymphocyte proliferation	0.0364814455963035
GO:0003725	double-stranded RNA binding	0.0364814455963035
GO:0007059	chromosome segregation	0.0392770992516106
GO:0042035	regulation of cytokine biosynthetic process	0.0392770992516106
GO:0031328	positive regulation of cellular biosynthetic process	0.0392770992516106
GO:0042113	B cell activation	0.0392944123856529
GO:0044454	nuclear chromosome part	0.041126194104434
GO:0042089	cytokine biosynthetic process	0.041126194104434
GO:0042107	cytokine metabolic process	0.041126194104434
GO:0051327	M phase of meiotic cell cycle	0.041126194104434
GO:0007126	meiosis	0.041126194104434
GO:0009891	positive regulation of biosynthetic process	0.041126194104434
GO:0051321	meiotic cell cycle	0.041126194104434
GO:0048522	positive regulation of cellular process	0.0420029648832667
GO:0051249	regulation of lymphocyte activation	0.0427493305344138
GO:0003723	RNA binding	0.0427493305344138
GO:0050865	regulation of cell activation	0.0436126357869517
GO:0007154	cell communication	0.0436126357869517
GO:0051247	positive regulation of protein metabolic process	0.0452925725332192
GO:0048518	positive regulation of biological process	0.0474896897675038

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
leukocyte	2.58e-56	140
hematopoietic stem cell	3.31e-52	172
angioblastic mesenchymal cell	3.31e-52	172
hematopoietic cell	1.71e-50	182
hematopoietic oligopotent progenitor cell	5.17e-49	165
hematopoietic multipotent progenitor cell	5.17e-49	165
nongranular leukocyte	4.27e-48	119
hematopoietic lineage restricted progenitor cell	2.69e-47	124
lymphocyte	1.05e-31	53
common lymphoid progenitor	1.05e-31	53
lymphoid lineage restricted progenitor cell	5.31e-31	52
myeloid leukocyte	1.46e-19	76
myeloid cell	3.54e-19	112
common myeloid progenitor	3.54e-19	112
lymphocyte of B lineage	6.77e-18	24
pro-B cell	6.77e-18	24
granulocyte monocyte progenitor cell	9.13e-18	71
myeloid lineage restricted progenitor cell	1.27e-16	70
macrophage dendritic cell progenitor	2.05e-16	65
monopoietic cell	1.00e-15	63
monocyte	1.00e-15	63
monoblast	1.00e-15	63
promonocyte	1.00e-15	63
CD14-positive, CD16-negative classical monocyte	5.97e-14	42
classical monocyte	7.74e-14	45
T cell	5.22e-13	25
pro-T cell	5.22e-13	25
B cell	6.97e-11	14
mature alpha-beta T cell	1.01e-10	18
alpha-beta T cell	1.01e-10	18
immature T cell	1.01e-10	18
mature T cell	1.01e-10	18
immature alpha-beta T cell	1.01e-10	18
CD8-positive, alpha-beta T cell	3.30e-07	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.52e-27	102
blood island	4.52e-27	102
hemolymphoid system	1.31e-25	112
bone marrow	2.32e-15	80
bone element	1.13e-13	86
adult organism	2.03e-12	115
immune system	2.66e-12	115
blood	3.44e-10	15
haemolymphatic fluid	3.44e-10	15
organism substance	3.44e-10	15
skeletal element	1.69e-08	101
skeletal system	1.69e-08	101

Disease

Ontology term	p-value	n
lymphoma	3.17e-07	10

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
BATF#10538	7	5.16680644079168	0.00032624169049433	0.00332737850718138
BCL11A#53335	7	6.01776320379544	0.000128319363723114	0.00170568232504496
EBF1#1879	25	6.74732336861288	9.95619081306104e-18	2.14837729819273e-15
IRF4#3662	10	6.64076142022549	1.36753689995089e-06	5.32727289421748e-05
MEF2A#4205	11	6.24774363654802	6.4050131274486e-07	2.90840506964176e-05
MEF2C#4208	7	8.7630145893445	1.19086481273547e-05	0.000301071726403486
NFKB1#4790	24	3.99131885395915	1.22269380056977e-11	1.51659047313191e-09
PAX5#5079	11	2.22318851039261	0.00674900907940991	0.0286831512673757
POLR2A#5430	29	1.88715582182376	8.87752431645193e-07	3.82807498796831e-05
POU2F2#5452	9	2.48348837938432	0.00764962989900298	0.0315105978158071
SPI1#6688	14	3.48062209452479	1.33337707023643e-05	0.00032551792388598
ZEB1#6935	9	4.60593600478469	9.33815167125314e-05	0.00135698792596912

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.