Coexpression cluster:C448

Full id: C448_Eosinophils_CD19_Neutrophils_immature_CD14_CD34_CD4

Phase1 CAGE Peaks

Hg19::chr11:64619474..64619518,+	p@chr11:64619474..64619518 +
Hg19::chr13:25861327..25861345,-	p@chr13:25861327..25861345 -
Hg19::chr13:25861383..25861392,-	p8@MTMR6
Hg19::chr13:25861424..25861442,-	p3@MTMR6
Hg19::chr13:25861448..25861459,-	p6@MTMR6
Hg19::chr13:25861474..25861481,-	p5@MTMR6
Hg19::chr13:25861499..25861517,-	p2@MTMR6
Hg19::chr15:55611198..55611219,+	p5@PIGB
Hg19::chr17:3817800..3817817,+	p@chr17:3817800..3817817 +
Hg19::chr19:18112074..18112107,+	p4@ARRDC2
Hg19::chr19:18112109..18112115,+	p10@ARRDC2
Hg19::chr1:172502624..172502648,-	p1@BC034700
Hg19::chr21:43934531..43934564,-	p@chr21:43934531..43934564 -
Hg19::chr22:50354104..50354157,+	p2@PIM3
Hg19::chr22:50628844..50628860,-	p@chr22:50628844..50628860 -
Hg19::chr2:158326065..158326081,-	p@chr2:158326065..158326081 -
Hg19::chr3:42054612..42054635,+	p@chr3:42054612..42054635 +
Hg19::chr6:30294289..30294313,+	p2@TRIM39
Hg19::chr6:33378569..33378612,+	p4@PHF1
Hg19::chr8:141608042..141608073,+	p1@BC078139
Hg19::chr9:88356530..88356542,+	p@chr9:88356530..88356542 +
Hg19::chrX:38186665..38186679,-	p8@RPGR

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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No GOStat results

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	1.64e-86	136
hematopoietic stem cell	5.47e-73	168
angioblastic mesenchymal cell	5.47e-73	168
hematopoietic cell	7.02e-69	177
nongranular leukocyte	7.25e-67	115
hematopoietic oligopotent progenitor cell	3.27e-66	161
hematopoietic multipotent progenitor cell	3.27e-66	161
hematopoietic lineage restricted progenitor cell	4.21e-66	120
classical monocyte	4.79e-46	42
CD14-positive, CD16-negative classical monocyte	4.79e-46	42
myeloid leukocyte	6.19e-45	72
granulocyte monocyte progenitor cell	2.05e-38	67
defensive cell	2.36e-38	48
phagocyte	2.36e-38	48
myeloid cell	1.31e-34	108
common myeloid progenitor	1.31e-34	108
macrophage dendritic cell progenitor	1.41e-34	61
myeloid lineage restricted progenitor cell	1.77e-33	66
monopoietic cell	2.63e-32	59
monocyte	2.63e-32	59
monoblast	2.63e-32	59
promonocyte	2.63e-32	59
lymphocyte	1.25e-28	53
common lymphoid progenitor	1.25e-28	53
lymphoid lineage restricted progenitor cell	7.81e-28	52
nucleate cell	4.39e-27	55
lymphocyte of B lineage	1.69e-18	24
pro-B cell	1.69e-18	24
mesenchymal cell	3.90e-18	354
B cell	1.79e-17	14
connective tissue cell	3.59e-17	361
stuff accumulating cell	8.06e-15	87
motile cell	7.92e-14	386
granulocyte	3.50e-12	8
intermediate monocyte	4.49e-12	9
CD14-positive, CD16-positive monocyte	4.49e-12	9
stem cell	3.80e-10	441
multi fate stem cell	6.80e-10	427
somatic stem cell	2.28e-09	433
CD4-positive, alpha-beta T cell	3.48e-09	6
mature alpha-beta T cell	9.27e-09	18
alpha-beta T cell	9.27e-09	18
immature T cell	9.27e-09	18
mature T cell	9.27e-09	18
immature alpha-beta T cell	9.27e-09	18
T cell	2.71e-08	25
pro-T cell	2.71e-08	25
blood cell	3.02e-08	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.00e-43	98
blood island	4.00e-43	98
hemolymphoid system	2.18e-38	108
bone marrow	8.38e-35	76
immune system	8.94e-34	93
bone element	6.00e-31	82
skeletal element	1.24e-26	90
skeletal system	2.99e-22	100
connective tissue	7.25e-16	371
lateral plate mesoderm	2.56e-11	203
musculoskeletal system	9.61e-08	167

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
CCNT2#905	13	3.74411911365974	4.52148768906304e-06	0.00014138312956828
CHD2#1106	9	4.23164570486599	0.00011305850948053	0.00154916264387787
CTCF#10664	11	2.68012818653751	0.000868568434253329	0.00648038424810569
CTCFL#140690	10	8.97567016317016	4.06420961939136e-08	2.68137705899946e-06
E2F1#1869	13	2.89982089970142	7.94249971490149e-05	0.00121646389166241
E2F6#1876	13	2.96468293236664	6.23302721693576e-05	0.00102081092913526
EBF1#1879	15	6.07259103175159	4.43514475306916e-10	4.33304099967999e-08
EGR1#1958	15	3.40103120100691	1.35216734815753e-06	5.32098740294742e-05
ELF1#1997	14	2.70969870105934	6.92225188485253e-05	0.00109921402554677
ELK4#2005	7	5.16589870951255	0.000250921929228307	0.00270388313729623
ETS1#2113	7	3.09551483888256	0.00511496570096734	0.0237835315811107
HEY1#23462	13	2.38733834365337	0.000631302257731059	0.00518419378008917
HMGN3#9324	9	3.34576952318888	0.000675510891091737	0.00545037715966702
MAX#4149	13	3.81287370986785	3.66862353649845e-06	0.000120373035981263
MYC#4609	14	3.32327028193326	5.92563771949817e-06	0.000177784452107633
NFKB1#4790	15	3.74186142558671	3.73038743635991e-07	1.83340203983996e-05
NRF1#4899	10	5.55012702168677	3.47417705175917e-06	0.000115701395761695
PAX5#5079	13	3.9411069047869	2.50523996824564e-06	8.82146854496312e-05
POLR2A#5430	22	2.14745317655807	4.97800844931664e-08	3.19544083858746e-06
RAD21#5885	7	3.29478351219065	0.00360558347202961	0.0182523160406815
REST#5978	10	4.3863766891491	2.82986167844788e-05	0.000596945917663944
SIN3A#25942	14	3.44201755342781	3.84586327170977e-06	0.000125557397384838
SMC3#9126	7	4.78702408702409	0.000400092655422489	0.00390626127322327
SPI1#6688	12	4.47508555010331	2.11279115254993e-06	7.6991554494474e-05
TAF1#6872	18	2.73521968833706	7.10005359864782e-07	3.17840762018508e-05
TBP#6908	16	2.69583322697919	1.01813841677941e-05	0.000266767080055256
TCF12#6938	11	5.31723245109321	1.33198496006276e-06	5.24947838656585e-05
TCF7L2#6934	8	3.91642784114085	0.000533487102311223	0.00461155930129795
YY1#7528	11	2.45558537492693	0.00185267117078072	0.010933555088725
ZEB1#6935	9	6.90890400717703	2.1839493953915e-06	7.83543424614541e-05
ZNF143#7702	8	4.9094096553556	0.000112150905487694	0.00154994421307785
ZNF263#10127	10	3.73720074409576	0.000113159736073697	0.00155034627781724

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.