Coexpression cluster:C2651

Full id: C2651_granulocyte_CD4_CD8_Small_CD19_CD34_Natural

Phase1 CAGE Peaks

Hg19::chr22:50683388..50683444,-	p1@TUBGCP6
Hg19::chr3:42642138..42642200,+	p1@NKTR
Hg19::chr6:131949305..131949389,-	p1@MED23
Hg19::chr8:100025476..100025548,+	p1@VPS13B

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:0008274	gamma-tubulin ring complex	0.0193637610957729
GO:0000931	gamma-tubulin large complex	0.0193637610957729
GO:0016018	cyclosporin A binding	0.0193637610957729
GO:0007020	microtubule nucleation	0.0193637610957729
GO:0000930	gamma-tubulin complex	0.0221270812370609
GO:0008144	drug binding	0.0363307709258282
GO:0044450	microtubule organizing center part	0.0363307709258282
GO:0000922	spindle pole	0.0428314809153511

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
hematopoietic stem cell	2.43e-24	172
angioblastic mesenchymal cell	2.43e-24	172
leukocyte	1.69e-22	140
hematopoietic oligopotent progenitor cell	1.68e-21	165
hematopoietic multipotent progenitor cell	1.68e-21	165
hematopoietic cell	6.18e-21	182
hematopoietic lineage restricted progenitor cell	1.03e-16	124
nongranular leukocyte	5.23e-16	119
lymphoid lineage restricted progenitor cell	1.33e-15	52
lymphocyte	1.77e-15	53
common lymphoid progenitor	1.77e-15	53
mature alpha-beta T cell	1.62e-11	18
alpha-beta T cell	1.62e-11	18
immature T cell	1.62e-11	18
mature T cell	1.62e-11	18
immature alpha-beta T cell	1.62e-11	18
T cell	6.96e-10	25
pro-T cell	6.96e-10	25
myeloid cell	2.35e-08	112
common myeloid progenitor	2.35e-08	112
CD8-positive, alpha-beta T cell	5.72e-08	11

Uber Anatomy

Ontology term	p-value	n
adult organism	8.66e-28	115
neural tube	3.55e-16	57
neural rod	3.55e-16	57
future spinal cord	3.55e-16	57
neural keel	3.55e-16	57
regional part of brain	1.11e-14	59
anterior neural tube	5.58e-14	42
regional part of forebrain	8.80e-14	41
forebrain	8.80e-14	41
future forebrain	8.80e-14	41
brain	9.52e-14	69
future brain	9.52e-14	69
central nervous system	9.26e-13	82
regional part of nervous system	3.83e-11	94
nervous system	3.83e-11	94
telencephalon	5.19e-11	34
gray matter	6.16e-11	34
brain grey matter	6.16e-11	34
regional part of telencephalon	8.34e-11	33
cerebral hemisphere	2.71e-10	32
neurectoderm	1.94e-08	90
cerebral cortex	3.77e-08	25
pallium	3.77e-08	25
regional part of cerebral cortex	3.94e-08	22
neural plate	1.23e-07	86
presumptive neural plate	1.23e-07	86
hematopoietic system	1.46e-07	102
blood island	1.46e-07	102
neocortex	1.50e-07	20

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
ATF3#467	2	11.2315872630044	0.0111955903992222	0.0411318910087018
BCLAF1#9774	2	10.8263238050609	0.0120220381643258	0.0436613570206913
BRCA1#672	2	10.0921153216119	0.013771396990026	0.0484755958962361
CCNT2#905	3	4.75215118272197	0.0138620699668949	0.0487307120829558
CHD2#1106	3	7.75801712558764	0.00335152246453634	0.017302503938394
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161065758323003
ELK4#2005	3	12.176761243851	0.000891263257762061	0.00663832858204335
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378712943474785
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186312581876019
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.0283034492699049
IRF4#3662	2	10.9572563433721	0.0117453018068803	0.0428575073512953
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0387026576552379
MEF2A#4205	3	14.057423182233	0.000583003885418661	0.00488866662298189
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186376899584795
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0435083657967821
POU2F2#5452	3	6.82959304330689	0.00486047377520374	0.0227664269008612
REST#5978	3	7.23752153709602	0.00410469730419261	0.019585639699953
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00797143127768839
SIX5#147912	3	12.8150365165942	0.000766447113693038	0.00601721191513096
STAT2#6773	2	32.6318855932203	0.00137958877512552	0.00898496333782327
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322670437000425
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244571960294585
TCF7L2#6934	4	10.7701765631373	7.42969445082454e-05	0.00115554707185356
THAP1#55145	2	15.6845723014257	0.00584046967835792	0.026250067252142
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0483139533475204
YY1#7528	4	4.91117074985386	0.0017187183805544	0.010694782468227
ZBTB33#10009	2	15.8323625149906	0.00573424893032464	0.0258416062150669
ZEB1#6935	3	12.6663240131579	0.00079333607591285	0.00613288130512674

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.