Coexpression cluster:C999

Full id: C999_CD14_Eosinophils_Mast_Neutrophils_CD19_CD8_CD4

Phase1 CAGE Peaks

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Hg19::chr11:65337828..65337854,-	p1@LOC254100
Hg19::chr11:82868189..82868212,+	p1@PCF11
Hg19::chr13:52027161..52027179,-	p1@INTS6
Hg19::chr16:89557354..89557392,+	p@chr16:89557354..89557392 +
Hg19::chr18:60193965..60193978,-	p@chr18:60193965..60193978 -
Hg19::chr19:47729523..47729537,+	p@chr19:47729523..47729537 +
Hg19::chr20:49126881..49126936,+	p1@PTPN1
Hg19::chr2:118771594..118771685,-	p1@CCDC93
Id	Short description

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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 ID	GO name	FDR corrected p-value
GO:0005654	nucleoplasm	9.89e-3
GO:0005849	mRNA cleavage factor complex	9.89e-3
GO:0006379	mRNA cleavage	9.89e-3
GO:0006396	RNA processing	9.89e-3
GO:0008286	insulin receptor signaling pathway	1.47e-2
GO:0016073	snRNA metabolic process	9.89e-3
GO:0016180	snRNA processing	9.89e-3
GO:0016591	DNA-directed RNA polymerase II, holoenzyme	4.62e-2
GO:0031974	membrane-enclosed lumen	1.35e-2
GO:0031981	nuclear lumen	9.89e-3

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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

Ontology term	p-value	n
myeloid leukocyte	1.29e-31	72
lymphocyte	1.62e-15	53
common lymphoid progenitor	1.62e-15	53
myeloid cell	1.69e-31	108
common myeloid progenitor	1.69e-31	108
leukocyte	1.85e-53	136
lymphoid lineage restricted progenitor cell	2.25e-15	52
monopoietic cell	2.29e-24	59
monocyte	2.29e-24	59
monoblast	2.29e-24	59
promonocyte	2.29e-24	59
macrophage dendritic cell progenitor	2.55e-25	61
hematopoietic oligopotent progenitor cell	3.02e-49	161
hematopoietic multipotent progenitor cell	3.02e-49	161
hematopoietic cell	3.47e-50	177
defensive cell	3.54e-25	48
phagocyte	3.54e-25	48
mature alpha-beta T cell	3.74e-09	18
alpha-beta T cell	3.74e-09	18
immature T cell	3.74e-09	18
mature T cell	3.74e-09	18
immature alpha-beta T cell	3.74e-09	18
T cell	3.76e-08	25
pro-T cell	3.76e-08	25
hematopoietic lineage restricted progenitor cell	3.82e-44	120
granulocyte monocyte progenitor cell	4.26e-28	67
myeloid lineage restricted progenitor cell	4.28e-27	66
nucleate cell	5.06e-16	55
lymphocyte of B lineage	5.43e-07	24
pro-B cell	5.43e-07	24
hematopoietic stem cell	5.64e-53	168
angioblastic mesenchymal cell	5.64e-53	168
nongranular leukocyte	6.43e-42	115
classical monocyte	7.36e-26	42
CD14-positive, CD16-negative classical monocyte	7.36e-26	42

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Uber Anatomy

Ontology term	p-value	n

Ontology term	p-value	n
skeletal system	1.09e-13	100
skeletal element	1.75e-16	90
hematopoietic system	5.17e-31	98
blood island	5.17e-31	98
blood	5.24e-07	15
haemolymphatic fluid	5.24e-07	15
organism substance	5.24e-07	15
bone marrow	5.33e-23	76
immune system	6.64e-21	93
bone element	8.36e-22	82
hemolymphoid system	9.49e-27	108

Showing 1 to 11 of 11 entries

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

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Motifs	-log10(p-value)

Motifs	-log10(p-value)
motif110_AGTCGCAGCG	2.18
motif152_GCKYRMKCGS	2.13
motif37_GCTCGCA	2.08
motif140_WTAAATAACG	2.05
motif169_GCCTGGCC	1.95
motif148_NTCSYSTYT	1.89
motif17_CGCTAN	1.82
motif141_TTAAACGGC	1.65
motif90_TTATATCGC	1.59
motif73_GAGCKMGC	1.56

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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	8.42369044725328	0.00417116638960993	0.0198728363927043
BRCA1#672	4	10.0921153216119	0.00035870656649756	0.00358703131926836
CCNT2#905	6	4.75215118272197	0.000323589541710397	0.00331164803005312
CHD2#1106	4	5.17201141705843	0.00443788460794178	0.0210065369184568
E2F1#1869	7	4.29396556301941	9.58670853279727e-05	0.00137097939539479
E2F4#1874	5	7.91753769705278	0.000139933401145107	0.00182590011021912
E2F6#1876	5	3.13572233231087	0.0102488050142096	0.0381554538508907
EGR1#1958	5	3.11761193425634	0.0105139099038836	0.0389273339638293
ELF1#1997	8	4.25809795880754	9.24826870984006e-06	0.000246775660650737
ELK4#2005	3	6.08838062192551	0.0103437704184363	0.0384172488880181
ETS1#2113	4	4.86438046110117	0.005553791515982	0.0251379228628605
FOS#2353	5	5.623722068059	0.00070970181512938	0.00570377436477855
FOXA1#3169	4	5.54070987469273	0.00344427292594616	0.017524915722152
GABPB1#2553	6	5.30076287713663	0.00017345294309267	0.00211158082802837
GTF2F1#2962	5	7.96228804797353	0.000136205383133915	0.00178126145869308
HEY1#23462	8	4.04011104310571	1.4081650274634e-05	0.000339569030947242
HMGN3#9324	5	5.11159232709412	0.00110951597588993	0.0077096965406499
IRF1#3659	6	5.72787281517293	0.000111198067191997	0.0015449534308188
IRF3#3661	2	11.7454880528724	0.0116448804945314	0.0425356629115965
MAX#4149	6	4.83941663175534	0.000291750431370536	0.00309813149993975
MXI1#4601	4	4.98078581437965	0.00509441532042917	0.0236995831470068
MYC#4609	6	3.91671140370705	0.000964927056924644	0.00694049703155323
NFKB1#4790	7	4.80205549616961	4.48248622098168e-05	0.00079414143924191
NFYA#4800	4	9.21279034991526	0.000508523135168021	0.00445625505234208
NFYB#4801	3	6.28492247007617	0.00947376901248262	0.0357001970735945
PBX3#5090	6	16.4358845150581	2.33030791475828e-07	1.227926479866e-05
POLR2A#5430	8	2.14745317655807	0.00221072578897191	0.0127315131334126
POU2F2#5452	6	6.82959304330689	4.02833503357943e-05	0.000738615313504217
RDBP#7936	2	38.4096009975062	0.00115478782065285	0.00789712448933755
REST#5978	5	6.03126794758001	0.000510547353254391	0.00443013085963238
RFX5#5993	4	6.02395541359755	0.0025264968061986	0.0139929363070783
SIN3A#25942	8	5.40888472681514	1.36410592556506e-06	5.35988934387092e-05
SP1#6667	6	4.27378603360567	0.000590472686428894	0.00494494241824611
SP2#6668	3	9.80757393519174	0.00270718466508561	0.0148902285252199
SREBF1#6720	3	17.6271935401831	0.000497260515006821	0.00439591932679849
SRF#6722	4	6.8985891310839	0.00152207190456878	0.00970237229255732
TAF1#6872	7	2.92516550002713	0.00126532535791574	0.00849397834267657
TAF7#6879	4	5.71653470246196	0.00306854155518016	0.0161782730820062
TAL1#6886	3	11.2007312540401	0.0018506999451652	0.0109324237315106
TBP#6908	6	2.78007801532229	0.00639018112126301	0.0278065133170946
TFAP2A#7020	3	6.19448788989186	0.00986148386238029	0.0370529397432413
TFAP2C#7022	4	5.40461430493011	0.00377514689654701	0.0186505471489344
USF1#7391	6	4.77112445790597	0.000316336110600381	0.00324090906955005
YY1#7528	7	4.29727440612212	9.53674534900876e-05	0.00136514274603224
ZBTB33#10009	3	11.8742718862429	0.00156455164595325	0.00992590264559054

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.