Coexpression cluster:C1644

Full id: C1644_Neutrophils_Eosinophils_medial_amygdala_frontal_paracentral_insula

Phase1 CAGE Peaks

Hg19::chr11:77122928..77123045,-	p1@PAK1
Hg19::chr12:90103081..90103155,-	p2@ATP2B1
Hg19::chr14:71788096..71788143,+	p3@SIPA1L1
Hg19::chr7:26331560..26331647,+	p1@SNX10
Hg19::chr7:26331652..26331663,+	p7@SNX10

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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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>

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Cell Type

Ontology term	p-value	n
leukocyte	2.60e-39	140
hematopoietic lineage restricted progenitor cell	8.90e-33	124
nongranular leukocyte	2.29e-32	119
myeloid leukocyte	4.45e-32	76
hematopoietic stem cell	1.02e-31	172
angioblastic mesenchymal cell	1.02e-31	172
hematopoietic oligopotent progenitor cell	4.56e-31	165
hematopoietic multipotent progenitor cell	4.56e-31	165
granulocyte monocyte progenitor cell	2.96e-28	71
macrophage dendritic cell progenitor	7.44e-27	65
myeloid lineage restricted progenitor cell	2.17e-26	70
hematopoietic cell	2.23e-26	182
monopoietic cell	4.20e-26	63
monocyte	4.20e-26	63
monoblast	4.20e-26	63
promonocyte	4.20e-26	63
CD14-positive, CD16-negative classical monocyte	2.56e-24	42
myeloid cell	1.16e-23	112
common myeloid progenitor	1.16e-23	112
classical monocyte	1.64e-23	45
lymphocyte of B lineage	1.63e-07	24
pro-B cell	1.63e-07	24
lymphoid lineage restricted progenitor cell	2.50e-07	52
lymphocyte	3.36e-07	53
common lymphoid progenitor	3.36e-07	53

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.21e-29	102
blood island	1.21e-29	102
bone marrow	1.28e-24	80
bone element	8.98e-24	86
hemolymphoid system	1.34e-22	112
neural tube	6.59e-20	57
neural rod	6.59e-20	57
future spinal cord	6.59e-20	57
neural keel	6.59e-20	57
skeletal element	8.02e-20	101
skeletal system	8.02e-20	101
regional part of forebrain	1.39e-18	41
forebrain	1.39e-18	41
future forebrain	1.39e-18	41
anterior neural tube	3.13e-18	42
adult organism	3.57e-16	115
telencephalon	5.60e-16	34
central nervous system	5.62e-16	82
gray matter	5.63e-16	34
brain grey matter	5.63e-16	34
cerebral hemisphere	9.46e-16	32
regional part of brain	1.68e-15	59
regional part of telencephalon	2.45e-15	33
regional part of cerebral cortex	7.27e-14	22
brain	7.95e-14	69
future brain	7.95e-14	69
immune system	6.87e-13	115
neocortex	8.87e-13	20
regional part of nervous system	1.29e-12	94
nervous system	1.29e-12	94
cerebral cortex	4.84e-12	25
pallium	4.84e-12	25
neural plate	9.06e-10	86
presumptive neural plate	9.06e-10	86
pre-chordal neural plate	1.19e-08	61
neurectoderm	6.34e-08	90

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
CTCF#10664	5	5.36025637307503	0.000225927829993709	0.00249452126405676
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00352256562139458
E2F6#1876	4	4.01372458535791	0.00663211823393388	0.0282888215737725
EGR1#1958	4	3.99054327584811	0.006780098300144	0.0287579371469252
ELF1#1997	4	3.40647836704603	0.0123506610529955	0.0447257520705199
PAX5#5079	5	6.66956553117783	7.57493746384605e-05	0.0011692564200216
RAD21#5885	4	8.28402711636506	0.000401162263912245	0.00386539216539634
SMARCB1#6598	3	10.9516294686944	0.00151187284834318	0.00965031710109483
SMC3#9126	3	9.0269597069597	0.00265096444946755	0.0146341813065142
ZEB1#6935	3	10.1330592105263	0.00189555692435707	0.0111595304184289

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.