Coexpression cluster:C4022

Full id: C4022_CD14_Eosinophils_Neutrophils_Basophils_migratory_epidermoid_Mast

Phase1 CAGE Peaks

Hg19::chr20:31407751..31407795,+	p1@MAPRE1
Hg19::chr8:101964198..101964221,-	p2@YWHAZ
Hg19::chr8:101964231..101964255,-	p1@YWHAZ

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:0031115	negative regulation of microtubule polymerization	0.00506284401442095
GO:0030981	cortical microtubule cytoskeleton	0.00506284401442095
GO:0051010	microtubule plus-end binding	0.00506284401442095
GO:0031113	regulation of microtubule polymerization	0.0101246447580706
GO:0046785	microtubule polymerization	0.0101246447580706
GO:0048523	negative regulation of cellular process	0.0140589016358978
GO:0048519	negative regulation of biological process	0.0140589016358978
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.0140589016358978
GO:0030863	cortical cytoskeleton	0.0140589016358978
GO:0031110	regulation of microtubule polymerization or depolymerization	0.0146766288835239
GO:0031109	microtubule polymerization or depolymerization	0.0147219867739274
GO:0044448	cell cortex part	0.0187912866763938
GO:0008017	microtubule binding	0.0187912866763938
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0187912866763938
GO:0005938	cell cortex	0.0209860622386991
GO:0015631	tubulin binding	0.0209860622386991
GO:0008022	protein C-terminus binding	0.0209860622386991
GO:0005819	spindle	0.0209860622386991
GO:0048770	pigment granule	0.0209860622386991
GO:0042470	melanosome	0.0209860622386991
GO:0051258	protein polymerization	0.0224198953551073
GO:0051128	regulation of cellular component organization and biogenesis	0.0224198953551073
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0224198953551073
GO:0019904	protein domain specific binding	0.0267419858021847
GO:0006916	anti-apoptosis	0.0343427151346421
GO:0043066	negative regulation of apoptosis	0.0411992843938898
GO:0043069	negative regulation of programmed cell death	0.0411992843938898
GO:0007067	mitosis	0.0411992843938898
GO:0000087	M phase of mitotic cell cycle	0.0411992843938898
GO:0051301	cell division	0.0411992843938898
GO:0005874	microtubule	0.0466903559920029
GO:0000279	M phase	0.0466903559920029
GO:0044444	cytoplasmic part	0.0466903559920029
GO:0007017	microtubule-based process	0.0466903559920029
GO:0000278	mitotic cell cycle	0.0469325831757985
GO:0016023	cytoplasmic membrane-bound vesicle	0.0479180146242358
GO:0031988	membrane-bound vesicle	0.0479180146242358
GO:0022403	cell cycle phase	0.0488980343754735

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	4.17e-28	136
classical monocyte	1.80e-25	42
CD14-positive, CD16-negative classical monocyte	1.80e-25	42
myeloid leukocyte	5.71e-25	72
defensive cell	1.23e-22	48
phagocyte	1.23e-22	48
granulocyte monocyte progenitor cell	2.79e-20	67
macrophage dendritic cell progenitor	8.98e-20	61
nongranular leukocyte	9.00e-20	115
hematopoietic lineage restricted progenitor cell	1.48e-19	120
stuff accumulating cell	3.66e-19	87
monopoietic cell	4.49e-19	59
monocyte	4.49e-19	59
monoblast	4.49e-19	59
promonocyte	4.49e-19	59
myeloid lineage restricted progenitor cell	2.74e-18	66
native cell	1.47e-15	722
hematopoietic stem cell	2.00e-14	168
angioblastic mesenchymal cell	2.00e-14	168
hematopoietic oligopotent progenitor cell	1.15e-13	161
hematopoietic multipotent progenitor cell	1.15e-13	161
animal cell	5.52e-13	679
eukaryotic cell	5.52e-13	679
hematopoietic cell	2.11e-12	177
somatic stem cell	1.48e-11	433
stem cell	3.80e-11	441
multi fate stem cell	4.06e-11	427
myeloid cell	5.74e-11	108
common myeloid progenitor	5.74e-11	108
somatic cell	3.53e-10	588
mesenchymal cell	2.08e-09	354
motile cell	4.40e-09	386
connective tissue cell	4.24e-08	361

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.29e-17	98
blood island	1.29e-17	98
hemolymphoid system	3.30e-15	108
bone marrow	8.76e-15	76
bone element	3.65e-14	82
skeletal element	2.28e-13	90
skeletal system	4.35e-13	100
immune system	2.34e-12	93
musculoskeletal system	6.16e-09	167
connective tissue	1.12e-07	371

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
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296284654763579
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190286271894525
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325820157324706
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322736893534468
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321100429163559
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00898473433069904
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00243257506694393
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108831329345889
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128245878465523
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156972517704835
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186809380496374
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174510824764174
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199889430300124
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246189226705661
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173095560223897
REST#5978	3	9.65002871612802	0.00111263624711459	0.00768688344330228
SREBF1#6720	2	31.3372329603255	0.0013381626513618	0.00887623811658148
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00614455819762868
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190560113399581

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.