Coexpression cluster:C1308

Full id: C1308_CD14_CD4_Basophils_Peripheral_Neutrophils_Eosinophils_CD8

Phase1 CAGE Peaks

Hg19::chr10:23727926..23727957,+	p4@OTUD1
Hg19::chr10:23727989..23728040,+	p2@OTUD1
Hg19::chr10:23728041..23728084,+	p3@OTUD1
Hg19::chr15:63796779..63796863,+	p1@USP3
Hg19::chr15:63796867..63796887,+	p2@USP3
Hg19::chr15:63796904..63796916,+	p4@USP3

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:0004221	ubiquitin thiolesterase activity	0.0316849169904627
GO:0004843	ubiquitin-specific protease activity	0.0316849169904627
GO:0019783	small conjugating protein-specific protease activity	0.0316849169904627
GO:0016790	thiolester hydrolase activity	0.0316849169904627
GO:0006511	ubiquitin-dependent protein catabolic process	0.0316849169904627
GO:0043632	modification-dependent macromolecule catabolic process	0.0316849169904627
GO:0019941	modification-dependent protein catabolic process	0.0316849169904627
GO:0051603	proteolysis involved in cellular protein catabolic process	0.0316849169904627
GO:0044257	cellular protein catabolic process	0.0316849169904627
GO:0008234	cysteine-type peptidase activity	0.0316849169904627
GO:0030163	protein catabolic process	0.0342956231334896
GO:0043285	biopolymer catabolic process	0.0400918403391028
GO:0044265	cellular macromolecule catabolic process	0.0415552303577736
GO:0006512	ubiquitin cycle	0.0415552303577736
GO:0009057	macromolecule catabolic process	0.0441540091840339

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	5.29e-40	136
hematopoietic lineage restricted progenitor cell	3.15e-33	120
nongranular leukocyte	1.01e-32	115
myeloid leukocyte	1.95e-31	72
defensive cell	7.14e-28	48
phagocyte	7.14e-28	48
granulocyte monocyte progenitor cell	9.78e-28	67
hematopoietic stem cell	3.72e-27	168
angioblastic mesenchymal cell	3.72e-27	168
classical monocyte	1.98e-26	42
CD14-positive, CD16-negative classical monocyte	1.98e-26	42
macrophage dendritic cell progenitor	2.18e-26	61
hematopoietic oligopotent progenitor cell	9.92e-26	161
hematopoietic multipotent progenitor cell	9.92e-26	161
myeloid lineage restricted progenitor cell	1.57e-25	66
monopoietic cell	1.79e-25	59
monocyte	1.79e-25	59
monoblast	1.79e-25	59
promonocyte	1.79e-25	59
hematopoietic cell	3.01e-23	177
myeloid cell	8.37e-18	108
common myeloid progenitor	8.37e-18	108
stuff accumulating cell	1.60e-09	87
mature alpha-beta T cell	3.52e-09	18
alpha-beta T cell	3.52e-09	18
immature T cell	3.52e-09	18
mature T cell	3.52e-09	18
immature alpha-beta T cell	3.52e-09	18
lymphoid lineage restricted progenitor cell	3.25e-08	52
lymphocyte	1.02e-07	53
common lymphoid progenitor	1.02e-07	53
nucleate cell	2.09e-07	55

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	3.94e-26	98
blood island	3.94e-26	98
hemolymphoid system	2.45e-24	108
bone marrow	1.05e-21	76
immune system	1.76e-21	93
bone element	3.93e-20	82
skeletal element	8.68e-17	90
skeletal system	1.56e-13	100

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
ATF3#467	3	11.2315872630044	0.00159345997118423	0.010038567132978
BCL11A#53335	3	14.1847275518035	0.000808083184942481	0.00616790175781684
BCLAF1#9774	3	10.8263238050609	0.00177235104699106	0.0108871056932537
BHLHE40#8553	3	22.4359067734887	0.000210319610478028	0.00244605454328672
CCNT2#905	6	6.33620157696263	1.54467812014647e-05	0.000362283041073383
CTCF#10664	6	5.36025637307503	4.21437267579784e-05	0.000754706563593365
E2F4#1874	6	12.6680603152844	2.41728555395527e-07	1.26736388538923e-05
E2F6#1876	6	5.01715573169739	6.26776799983417e-05	0.00102425195139208
EGR1#1958	6	4.98817909481014	6.48943962979974e-05	0.0010543724105424
ELF1#1997	6	4.25809795880754	0.000167722477628883	0.00205066352623307
ELK4#2005	3	8.11784082923401	0.00405611313418576	0.019405240477381
FOSL2#2355	3	8.46510030228085	0.00359831563461509	0.0182181736747899
FOXA1#3169	6	11.0814197493855	5.39600313513231e-07	2.50245635626147e-05
FOXA2#3170	3	12.3152318763326	0.00121971244012452	0.0082041313540391
GTF2B#2959	3	15.9719149671621	0.000571165371589299	0.00486636810600545
GTF2F1#2962	3	6.36983043837883	0.00806820819630316	0.03191076254691
HDAC2#3066	6	13.4156202366263	1.71355402088576e-07	9.4190457045941e-06
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.00252872013691396
HMGN3#9324	6	8.17854772335059	3.33956428934731e-06	0.000111467163571474
HNF4A#3172	3	11.5661451814768	0.00146348715008573	0.00937527660355786
HNF4G#3174	3	14.3767112632234	0.000776977293719738	0.00608889709452958
IRF1#3659	6	7.6371637535639	5.03701715640675e-06	0.000155455388533677
IRF4#3662	3	10.9572563433721	0.00171175344181094	0.0106877394457639
JUN#3725	3	6.25641459616817	0.00848634685095487	0.0324048692467141
MAX#4149	6	6.45255550900712	1.3848964723355e-05	0.000334266703661307
MEF2A#4205	3	9.37161545482203	0.00268739994710391	0.0147969929921755
MEF2C#4208	3	20.655677246312	0.000268356349406041	0.0028654400138654
MXI1#4601	6	9.9615716287593	1.02262624227062e-06	4.2978697028773e-05
MYC#4609	6	5.2222818716094	4.92821127172503e-05	0.00085313684237973
NR3C1#2908	3	7.48651166558652	0.0051086696598407	0.0237553139182593
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0379821444324154
RFX5#5993	3	6.02395541359755	0.00943790403633506	0.0355997276672492
RXRA#6256	3	10.0373085695666	0.00220541911678922	0.0127037541855578
SIN3A#25942	6	5.40888472681514	3.99207083571449e-05	0.000741864565856202
SMC3#9126	6	15.0449328449328	8.61317699636729e-08	5.12565009870999e-06
SRF#6722	3	6.8985891310839	0.0064424516893037	0.0279966384545911
STAT1#6772	3	10.3532937485996	0.00201668045992093	0.0117199983614536
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00572422445525758
TCF12#6938	3	5.31723245109321	0.01336734573386	0.0472364141802944
TCF7L2#6934	6	10.7701765631373	6.40204410218762e-07	2.90832137446008e-05
USF1#7391	6	6.36149927720796	1.50818327938273e-05	0.000356849011136052
USF2#7392	3	6.4960986925348	0.00763431981530056	0.0314524941692377
ZEB1#6935	3	8.44421600877193	0.00362384381073359	0.0183332020804691
ZNF263#10127	6	8.22184163701068	3.23542093046082e-06	0.000108615919818836

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.