Coexpression cluster:C3904

Full id: C3904_CD14_Mast_CD19_Neutrophils_CD4_Eosinophils_CD8

Phase1 CAGE Peaks

Hg19::chr1:171454639..171454657,+	p2@PRRC2C
Hg19::chr1:171454659..171454723,+	p1@PRRC2C
Hg19::chr7:23571586..23571610,-	p1@TRA2A

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0000375	RNA splicing, via transesterification reactions	0.0185446838572942
GO:0000398	nuclear mRNA splicing, via spliceosome	0.0185446838572942
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0185446838572942
GO:0008380	RNA splicing	0.0413281525962557
GO:0006397	mRNA processing	0.0413281525962557
GO:0016071	mRNA metabolic process	0.0413281525962557
GO:0042802	identical protein binding	0.0413281525962557

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>

---

Cell Type

Ontology term	p-value	n
hematopoietic stem cell	2.13e-31	168
angioblastic mesenchymal cell	2.13e-31	168
leukocyte	2.62e-31	136
hematopoietic oligopotent progenitor cell	2.32e-29	161
hematopoietic multipotent progenitor cell	2.32e-29	161
hematopoietic cell	1.66e-28	177
nongranular leukocyte	2.07e-23	115
hematopoietic lineage restricted progenitor cell	6.01e-23	120
myeloid cell	9.35e-18	108
common myeloid progenitor	9.35e-18	108
myeloid leukocyte	2.96e-16	72
classical monocyte	4.07e-15	42
CD14-positive, CD16-negative classical monocyte	4.07e-15	42
granulocyte monocyte progenitor cell	6.72e-14	67
macrophage dendritic cell progenitor	4.67e-12	61
defensive cell	7.19e-12	48
phagocyte	7.19e-12	48
myeloid lineage restricted progenitor cell	7.82e-12	66
monopoietic cell	2.40e-11	59
monocyte	2.40e-11	59
monoblast	2.40e-11	59
promonocyte	2.40e-11	59
lymphocyte	5.09e-11	53
common lymphoid progenitor	5.09e-11	53
lymphoid lineage restricted progenitor cell	1.02e-10	52
nucleate cell	4.32e-10	55

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.89e-14	98
blood island	2.89e-14	98
hemolymphoid system	1.26e-11	108
bone element	1.69e-10	82
bone marrow	3.32e-10	76
immune system	8.43e-09	93
skeletal element	5.39e-08	90
skeletal system	8.34e-07	100

Disease

Ontology term	p-value	n
cancer	1.50e-08	235
disease of cellular proliferation	4.88e-08	239
cell type cancer	8.56e-07	143

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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	2	14.9754496840058	0.00576829454079388	0.0259580710766103
BHLHE40#8553	2	29.9145423646516	0.00146748352710614	0.00939741934437664
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164252263779961
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190127641249189
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325532086454351
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437392186792864
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322409727313636
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376780124480053
GATA3#2625	2	18.1576775714707	0.00394454681927962	0.0189522254799993
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000627933151014351
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434087502517998
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108763119863648
IRF4#3662	2	14.6096751244961	0.00605612247321789	0.0268393182967158
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186638958533085
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294667216285865
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174485304023495
NFE2#4778	2	51.469507101086	0.000498765352839211	0.00440661151215417
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269742715158927
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00882655658402661
PRDM1#639	2	87.8873038516405	0.000171624884802908	0.00209176465677803
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00484819308418801
SIRT6#51548	2	102.425602660017	0.000126437939273122	0.0016828153357647
SMARCC1#6599	2	29.1089062130876	0.00154920081422414	0.00984286311210334
SMARCC2#6601	2	62.7702496179317	0.000335837541708507	0.00341757156956979
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457521639683689
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246671529984317
STAT1#6772	2	13.8043916647995	0.00677093170844408	0.0287529209033988
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00543324973571105
TAL1#6886	2	19.9124111182935	0.00328717660874055	0.0170140468748267
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00197117755259636
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190390178068942
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329601149410465

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

---

This analysis result is provided for C0 - C305 clusters.