Coexpression cluster:C1207

Full id: C1207_migratory_granulocyte_CD19_CD14_immature_adult_Dendritic

Phase1 CAGE Peaks

Hg19::chr15:45028225..45028238,+	p13@TRIM69
Hg19::chr16:10971037..10971076,+	p1@CIITA
Hg19::chr16:10971077..10971090,+	p2@CIITA
Hg19::chr16:10971094..10971117,+	p3@CIITA
Hg19::chr16:10971144..10971153,+	p4@CIITA
Hg19::chr16:11004975..11004985,+	p@chr16:11004975..11004985 +
Hg19::chr4:185395590..185395627,-	p3@IRF2

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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p.value	FDR	nGenes	nPathway	Name
9.01000184573147e-06	0.00570333116834802	2	50	Type II interferon signaling (IFNG) (Wikipathways):WP619
6.25100917324437e-05	0.0197844440333184	2	131	IL-5 up reg. targets (Netpath):NetPath_17

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:0003702	RNA polymerase II transcription factor activity	0.0164432371661441
GO:0043130	ubiquitin binding	0.0386029895776261
GO:0032182	small conjugating protein binding	0.0386029895776261

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
leukocyte	4.25e-57	136
nongranular leukocyte	1.83e-56	115
hematopoietic stem cell	8.48e-50	168
angioblastic mesenchymal cell	8.48e-50	168
hematopoietic lineage restricted progenitor cell	1.08e-49	120
hematopoietic cell	3.42e-49	177
hematopoietic oligopotent progenitor cell	7.63e-46	161
hematopoietic multipotent progenitor cell	7.63e-46	161
macrophage dendritic cell progenitor	1.25e-38	61
monopoietic cell	1.23e-36	59
monocyte	1.23e-36	59
monoblast	1.23e-36	59
promonocyte	1.23e-36	59
defensive cell	1.84e-36	48
phagocyte	1.84e-36	48
granulocyte monocyte progenitor cell	6.28e-35	67
classical monocyte	7.79e-34	42
CD14-positive, CD16-negative classical monocyte	7.79e-34	42
myeloid lineage restricted progenitor cell	1.85e-30	66
myeloid leukocyte	4.47e-30	72
myeloid cell	8.04e-27	108
common myeloid progenitor	8.04e-27	108
lymphocyte of B lineage	2.29e-20	24
pro-B cell	2.29e-20	24
lymphocyte	4.07e-17	53
common lymphoid progenitor	4.07e-17	53
lymphoid lineage restricted progenitor cell	1.72e-16	52
nucleate cell	5.57e-16	55
B cell	1.34e-13	14
stuff accumulating cell	2.63e-13	87
dendritic cell	1.28e-11	10
conventional dendritic cell	4.92e-10	8
intermediate monocyte	8.87e-08	9
CD14-positive, CD16-positive monocyte	8.87e-08	9
immature conventional dendritic cell	7.41e-07	5
common dendritic progenitor	7.41e-07	5
Langerhans cell	8.99e-07	5
circulating cell	9.14e-07	6
mesenchymal cell	9.28e-07	354

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	3.15e-46	98
blood island	3.15e-46	98
hemolymphoid system	4.84e-42	108
bone marrow	2.30e-31	76
immune system	3.54e-31	93
bone element	2.23e-27	82
adult organism	2.34e-25	114
skeletal element	5.97e-23	90
skeletal system	5.79e-20	100
lateral plate mesoderm	9.11e-13	203
blood	2.91e-12	15
haemolymphatic fluid	2.91e-12	15
organism substance	2.91e-12	15

Disease

Ontology term	p-value	n
lymphoma	3.42e-07	10

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	5	17.3984298516455	2.2818035468994e-06	8.14454137507269e-05
BCL11A#53335	4	16.2111172020612	4.9553880252627e-05	0.00084897600060763
E2F1#1869	5	3.50527801062809	0.00509055358791505	0.0236890044186722
EBF1#1879	4	5.08940962661086	0.00419823316250242	0.0199944946535907
FAM48A#55578	4	660.096428571429	1.88892317757448e-11	2.27540078134604e-09
IRF3#3661	4	26.8468298351369	6.81330236493166e-06	0.000198154966775577
IRF4#3662	4	12.5225786781395	0.000135673113103555	0.00177652510775103
MEF2A#4205	5	13.3880220783172	8.2817757531295e-06	0.000229001953370689
NFKB1#4790	5	3.9200453029956	0.00303658142448461	0.0161188069830621
PAX5#5079	5	4.76397537941274	0.00121882104700747	0.00820024810464555
POU2F2#5452	5	6.50437432695895	0.000276785134033055	0.00294820628386316
REST#5978	4	5.51430212350173	0.00311564137576196	0.0163769927849013
RXRA#6256	4	11.4712097937904	0.000190695857178501	0.00230510238748443
SMC3#9126	4	8.59710448281877	0.000579846628016137	0.00486688113665333
SP1#6667	5	4.07027241295778	0.00254920612899158	0.0141097323072633
SPI1#6688	6	7.03227729301948	2.05436318006376e-05	0.000455145600684511
TCF12#6938	5	7.59604635870459	0.000131112637393808	0.00172437636780908
TCF7L2#6934	5	7.69298325938382	0.000123319885015426	0.00165928954794203
YY1#7528	5	3.50797910703847	0.00507257067280898	0.0236147904295934
ZNF143#7702	4	7.71478660127309	0.000877196960661348	0.00654149042302824

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.