Coexpression cluster:C686

Full id: C686_CD14_immature_CD19_Eosinophils_migratory_Mast_Basophils

Phase1 CAGE Peaks

Hg19::chr11:62572901..62572919,-	p1@NXF1
Hg19::chr11:65153902..65153912,-	p@chr11:65153902..65153912 -
Hg19::chr11:9482656..9482660,+	p@chr11:9482656..9482660 +
Hg19::chr12:111020479..111020516,-	p@chr12:111020479..111020516 -
Hg19::chr12:111020600..111020632,+	p@chr12:111020600..111020632 +
Hg19::chr13:41635806..41635828,-	p14@ELF1
Hg19::chr1:200638744..200638765,+	p1@ENST00000422640
Hg19::chr1:6845035..6845053,-	p1@ENST00000442889
Hg19::chr4:106394656..106394684,+	p@chr4:106394656..106394684 +
Hg19::chr6:112126045..112126050,+	p@chr6:112126045..112126050 +
Hg19::chr6:14117995..14118012,+	p1@CD83
Hg19::chr7:151047008..151047012,-	p@chr7:151047008..151047012 -

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:0016973	poly(A)+ mRNA export from nucleus	0.00794725374557758
GO:0050858	negative regulation of antigen receptor-mediated signaling pathway	0.00794725374557758
GO:0050860	negative regulation of T cell receptor signaling pathway	0.00794725374557758
GO:0042405	nuclear inclusion body	0.00794725374557758
GO:0016234	inclusion body	0.0105950906474368
GO:0050856	regulation of T cell receptor signaling pathway	0.0105950906474368
GO:0005487	nucleocytoplasmic transporter activity	0.0105950906474368
GO:0050854	regulation of antigen receptor-mediated signaling pathway	0.0132426936896461
GO:0050852	T cell receptor signaling pathway	0.0200070579879434
GO:0006406	mRNA export from nucleus	0.0211733427389052
GO:0050851	antigen receptor-mediated signaling pathway	0.0211733427389052
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0211733427389052
GO:0006405	RNA export from nucleus	0.0211733427389052
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0211733427389052
GO:0002757	immune response-activating signal transduction	0.0211733427389052
GO:0002764	immune response-regulating signal transduction	0.0211733427389052
GO:0003729	mRNA binding	0.0211733427389052
GO:0006955	immune response	0.0228402138005044
GO:0001817	regulation of cytokine production	0.0228402138005044
GO:0051168	nuclear export	0.0232838193519774
GO:0002376	immune system process	0.027740075393911
GO:0002253	activation of immune response	0.0308132798303632
GO:0006959	humoral immune response	0.0308132798303632
GO:0051028	mRNA transport	0.0308132798303632
GO:0050778	positive regulation of immune response	0.0308132798303632
GO:0002684	positive regulation of immune system process	0.0308132798303632
GO:0005643	nuclear pore	0.0308132798303632
GO:0050658	RNA transport	0.0308132798303632
GO:0051236	establishment of RNA localization	0.0308132798303632
GO:0050657	nucleic acid transport	0.0308132798303632
GO:0006403	RNA localization	0.0308132798303632
GO:0046930	pore complex	0.0308132798303632
GO:0050776	regulation of immune response	0.0308132798303632
GO:0002682	regulation of immune system process	0.0308132798303632
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0308132798303632
GO:0051240	positive regulation of multicellular organismal process	0.0308132798303632
GO:0044453	nuclear membrane part	0.0314082394328219
GO:0001816	cytokine production	0.0314082394328219
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0376154392284251
GO:0031965	nuclear membrane	0.0391808275779859
GO:0006913	nucleocytoplasmic transport	0.0391808275779859
GO:0051169	nuclear transport	0.0391808275779859
GO:0005635	nuclear envelope	0.0475384409643424

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	1.81e-59	140
hematopoietic stem cell	5.65e-56	172
angioblastic mesenchymal cell	5.65e-56	172
hematopoietic cell	4.68e-53	182
hematopoietic oligopotent progenitor cell	7.04e-52	165
hematopoietic multipotent progenitor cell	7.04e-52	165
hematopoietic lineage restricted progenitor cell	4.21e-48	124
nongranular leukocyte	1.89e-46	119
myeloid leukocyte	2.85e-32	76
myeloid cell	1.09e-30	112
common myeloid progenitor	1.09e-30	112
granulocyte monocyte progenitor cell	2.07e-29	71
myeloid lineage restricted progenitor cell	5.05e-27	70
CD14-positive, CD16-negative classical monocyte	2.56e-26	42
macrophage dendritic cell progenitor	2.65e-26	65
classical monocyte	2.90e-26	45
monopoietic cell	5.53e-25	63
monocyte	5.53e-25	63
monoblast	5.53e-25	63
promonocyte	5.53e-25	63
lymphocyte	1.07e-18	53
common lymphoid progenitor	1.07e-18	53
lymphoid lineage restricted progenitor cell	2.17e-18	52
lymphocyte of B lineage	1.29e-09	24
pro-B cell	1.29e-09	24
mesenchymal cell	5.44e-09	358
T cell	2.48e-08	25
pro-T cell	2.48e-08	25
motile cell	6.69e-08	390
connective tissue cell	6.90e-08	365
mature alpha-beta T cell	3.68e-07	18
alpha-beta T cell	3.68e-07	18
immature T cell	3.68e-07	18
mature T cell	3.68e-07	18
immature alpha-beta T cell	3.68e-07	18
dendritic cell	7.75e-07	10
B cell	8.44e-07	14

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	5.06e-33	102
blood island	5.06e-33	102
hemolymphoid system	3.13e-29	112
bone marrow	8.37e-26	80
bone element	2.70e-23	86
immune system	4.60e-18	115
skeletal element	1.44e-15	101
skeletal system	1.44e-15	101
connective tissue	1.23e-07	375

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
BCL3#602	4	11.5157009345794	0.000288024998630705	0.00306168374880328
CCNT2#905	7	3.69611758656154	0.000922226403861466	0.00670446912104188
CHD2#1106	6	5.17201141705843	0.000449789536324633	0.00418378779695478
E2F1#1869	9	3.68054191115949	7.26432475498673e-05	0.00114172883835374
E2F4#1874	5	5.27835846470185	0.0015115503118649	0.00965179769019675
E2F6#1876	9	3.76286679877304	6.04050132232551e-05	0.000991612570893357
EBF1#1879	6	4.4532334232845	0.00101188147698625	0.0071798280844464
EGR1#1958	8	3.32545272987342	0.000590880184228549	0.00494637187885904
ELF1#1997	11	3.90325646224024	1.12752972864617e-06	4.6361447767747e-05
ESRRA#2101	2	80.640052356021	0.000277364887957792	0.00295377908977504
FAM48A#55578	1	96.2640625	0.0103390814161557	0.0384011993321912
GABPB1#2553	6	3.53384191809109	0.00343277026857388	0.0174680907269337
GATA1#2623	4	4.52010271460015	0.0090402565551404	0.0342209262182787
GTF2B#2959	3	7.98595748358106	0.00545549118698288	0.024717628045521
HDAC2#3066	4	4.47187341220875	0.00938675858650172	0.0354208794311397
HEY1#23462	7	2.35673144181166	0.0134698206126472	0.0475792131418222
HMGN3#9324	5	3.40772821806275	0.0102804055907503	0.0381954919776723
IRF1#3659	7	4.45501218957894	0.000285027758631937	0.00303136599630966
MAX#4149	6	3.22627775450356	0.0054834811269129	0.024833670934203
MYC#4609	8	3.4815212477396	0.000425379627013113	0.00397514520988032
NFKB1#4790	12	5.48806342419384	1.33744036073436e-09	1.20414598133393e-07
PAX5#5079	9	5.00217414838337	5.4522949797447e-06	0.000165340370322171
PBX3#5090	4	7.30483756224804	0.00159577918440949	0.0100525714603138
POLR2A#5430	12	2.14745317655807	0.000103929203846201	0.00145265820670415
RFX5#5993	4	4.0159702757317	0.0136387877569436	0.0481207173591243
SIN3A#25942	6	2.70444236340757	0.0132549134278075	0.0468851149321542
SP1#6667	7	3.32405580391552	0.00177269703194813	0.0108885905616439
SPI1#6688	7	4.78585537997159	0.000180403719972232	0.0021870207905026
STAT1#6772	5	8.62774479049967	0.000156089170822523	0.00196857830111502
TAF1#6872	10	2.78587190478774	0.00020079712338388	0.00239368231584169
TAL1#6886	3	7.46715416936005	0.0065753637007261	0.0280972304545695
TBP#6908	11	3.39787312983835	4.97194305024537e-06	0.000153537776530034
TCF12#6938	6	5.31723245109321	0.000386542592763444	0.00378280751926737
TCF7L2#6934	6	5.38508828156867	0.000360576308593949	0.00360503820536506
TFAP2C#7022	7	6.3053833557518	3.01291531004594e-05	0.00061990910572476
ZBTB7A#51341	7	4.28861376292761	0.000362912992175886	0.00362423694682132
ZNF274#10782	1	118.478846153846	0.00840799969553707	0.0330369857111436

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.