Coexpression cluster:C2578

Full id: C2578_Eosinophils_CD14_CD19_Neutrophils_CD4_Whole_CD14CD16

Phase1 CAGE Peaks

Hg19::chr1:2487990..2488033,+	p1@TNFRSF14
Hg19::chr2:231191875..231191918,+	p1@SP140L
Hg19::chr2:231280908..231280945,+	p1@SP100
Hg19::chr7:144533074..144533153,-	p1@TPK1

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:0009229	thiamin diphosphate biosynthetic process	0.0052451874720812
GO:0006772	thiamin metabolic process	0.0052451874720812
GO:0042724	thiamin and derivative biosynthetic process	0.0052451874720812
GO:0042357	thiamin diphosphate metabolic process	0.0052451874720812
GO:0004788	thiamin diphosphokinase activity	0.0052451874720812
GO:0042723	thiamin and derivative metabolic process	0.00728455370169519
GO:0005031	tumor necrosis factor receptor activity	0.00971130870574048
GO:0043120	tumor necrosis factor binding	0.00971130870574048
GO:0005035	death receptor activity	0.00971130870574048
GO:0016778	diphosphotransferase activity	0.0122348080968153
GO:0016605	PML body	0.0127107404706818
GO:0006767	water-soluble vitamin metabolic process	0.0465402161415903

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	4.21e-55	136
hematopoietic lineage restricted progenitor cell	1.69e-46	120
nongranular leukocyte	3.42e-46	115
hematopoietic stem cell	1.61e-45	168
angioblastic mesenchymal cell	1.61e-45	168
hematopoietic cell	1.76e-43	177
hematopoietic oligopotent progenitor cell	1.15e-42	161
hematopoietic multipotent progenitor cell	1.15e-42	161
myeloid leukocyte	1.13e-31	72
granulocyte monocyte progenitor cell	1.31e-27	67
myeloid lineage restricted progenitor cell	4.76e-27	66
macrophage dendritic cell progenitor	1.10e-25	61
defensive cell	1.78e-25	48
phagocyte	1.78e-25	48
monopoietic cell	1.94e-25	59
monocyte	1.94e-25	59
monoblast	1.94e-25	59
promonocyte	1.94e-25	59
classical monocyte	2.15e-23	42
CD14-positive, CD16-negative classical monocyte	2.15e-23	42
myeloid cell	4.79e-23	108
common myeloid progenitor	4.79e-23	108
mesenchymal cell	3.61e-21	354
connective tissue cell	2.89e-20	361
nucleate cell	2.40e-18	55
lymphocyte	2.78e-18	53
common lymphoid progenitor	2.78e-18	53
lymphoid lineage restricted progenitor cell	4.78e-18	52
multi fate stem cell	8.09e-16	427
somatic stem cell	4.70e-14	433
motile cell	3.94e-13	386
stem cell	4.72e-13	441
mature alpha-beta T cell	4.73e-10	18
alpha-beta T cell	4.73e-10	18
immature T cell	4.73e-10	18
mature T cell	4.73e-10	18
immature alpha-beta T cell	4.73e-10	18
T cell	1.66e-09	25
pro-T cell	1.66e-09	25
lymphocyte of B lineage	1.27e-08	24
pro-B cell	1.27e-08	24
B cell	4.45e-08	14
stuff accumulating cell	5.04e-08	87
CD8-positive, alpha-beta T cell	7.30e-07	11

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.30e-35	108
hematopoietic system	1.40e-34	98
blood island	1.40e-34	98
immune system	6.22e-29	93
bone marrow	1.31e-25	76
bone element	8.91e-22	82
skeletal element	3.39e-20	90
connective tissue	1.49e-19	371
lateral plate mesoderm	1.42e-18	203
skeletal system	1.85e-18	100
musculoskeletal system	3.05e-10	167
mesoderm	1.41e-09	315
mesoderm-derived structure	1.41e-09	315
presumptive mesoderm	1.41e-09	315
blood	1.93e-07	15
haemolymphatic fluid	1.93e-07	15
organism substance	1.93e-07	15

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
BATF#10538	2	12.1789008961518	0.00956675880504781	0.0360207196928541
FOS#2353	3	6.7484664816708	0.00503245277631794	0.0234698729796315
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378631596048413
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00307731073298192
IRF4#3662	2	10.9572563433721	0.0117453018068803	0.0428470283771272
NR2C2#7182	2	16.3073054526204	0.00541182534464822	0.0245581415237765
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0435007930662852
POLR3A#11128	1	84.7830275229358	0.0117428417771162	0.0428635066531607
PRDM1#639	2	65.9154778887304	0.000341517512076895	0.00346760134588751
REST#5978	3	7.23752153709602	0.00410469730419261	0.0195829556325692
SPI1#6688	3	6.15324263139204	0.00658038711305903	0.0281014495297993
SRF#6722	3	10.3478836966259	0.00143989377840126	0.00923943636780839
STAT1#6772	2	10.3532937485996	0.0131077747617126	0.0464937810195117
STAT2#6773	2	32.6318855932203	0.00137958877512552	0.00898384287849694
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322483756838625
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.034247234708881

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.