Coexpression cluster:C4328

Full id: C4328_Reticulocytes_Mast_small_Melanocyte_CD4_CD19_Macrophage

Phase1 CAGE Peaks

Hg19::chr3:42623743..42623756,-	p4@SEC22C
Hg19::chr3:42623766..42623775,-	p9@SEC22C
Hg19::chr3:42623776..42623801,-	p3@SEC22C

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

---

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>

---

Cell Type

Ontology term	p-value	n
myeloid leukocyte	6.03e-30	76
myeloid cell	1.67e-29	112
common myeloid progenitor	1.67e-29	112
hematopoietic stem cell	8.20e-28	172
angioblastic mesenchymal cell	8.20e-28	172
myeloid lineage restricted progenitor cell	1.11e-27	70
granulocyte monocyte progenitor cell	4.75e-27	71
hematopoietic oligopotent progenitor cell	1.64e-26	165
hematopoietic multipotent progenitor cell	1.64e-26	165
hematopoietic cell	1.73e-26	182
leukocyte	6.20e-26	140
macrophage dendritic cell progenitor	4.47e-24	65
hematopoietic lineage restricted progenitor cell	1.75e-23	124
monopoietic cell	5.16e-23	63
monocyte	5.16e-23	63
monoblast	5.16e-23	63
promonocyte	5.16e-23	63
nongranular leukocyte	1.34e-19	119
classical monocyte	1.64e-19	45
CD14-positive, CD16-negative classical monocyte	4.20e-19	42
mesenchymal cell	3.93e-12	358
connective tissue cell	4.20e-11	365
motile cell	6.05e-10	390
multi fate stem cell	9.47e-07	430

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.35e-24	102
blood island	1.35e-24	102
bone marrow	2.82e-24	80
hemolymphoid system	2.24e-23	112
bone element	5.20e-21	86
skeletal element	9.99e-19	101
skeletal system	9.99e-19	101
immune system	2.48e-17	115
connective tissue	4.72e-10	375
lateral plate mesoderm	2.18e-08	216
musculoskeletal system	5.32e-07	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

---

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190657441475594
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280554087405244
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00172147611892546
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326711594143652
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.0043813839883209
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323481777809339
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00917704595295246
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321714294020108
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463927327814344
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00388821060019958
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00438067608049067
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108961785303207
JUNB#3726	3	30.6106326598211	3.4847716247536e-05	0.000681674590218471
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157255642575728
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187115124163308
MYC#4609	3	5.2222818716094	0.00702084375574015	0.029545084253596
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.027031977898564
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.0066661753051538
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277661591223265
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203551128958471
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00310119015958549
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247352614543593
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000720931851619159
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.0063058764762344
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.0024900488065501
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00617673013316212
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190873947578434
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00422517746801142
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109742625163352

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.