Coexpression cluster:C2564

Full id: C2564_optic_CD14_spinal_corpus_thalamus_substantia_locus

Phase1 CAGE Peaks

Hg19::chr1:212732307..212732355,-	p1@uc001hje.2
Hg19::chr4:56261764..56261833,+	p3@TMEM165
Hg19::chr6:161695042..161695064,-	p2@AGPAT4
Hg19::chr6:161695074..161695112,-	p1@AGPAT4

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:0003841	1-acylglycerol-3-phosphate O-acyltransferase activity	0.0103591865847246
GO:0016411	acylglycerol O-acyltransferase activity	0.0103591865847246
GO:0008374	O-acyltransferase activity	0.0151029214517312
GO:0008654	phospholipid biosynthetic process	0.0292229120021243
GO:0046467	membrane lipid biosynthetic process	0.0292229120021243
GO:0006644	phospholipid metabolic process	0.0381709954969072
GO:0008415	acyltransferase activity	0.0381709954969072
GO:0016747	transferase activity, transferring groups other than amino-acyl groups	0.0381709954969072
GO:0006643	membrane lipid metabolic process	0.0381709954969072
GO:0016746	transferase activity, transferring acyl groups	0.0381709954969072
GO:0008610	lipid biosynthetic process	0.0390171657311839

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
defensive cell	1.50e-26	48
phagocyte	1.50e-26	48
granulocyte monocyte progenitor cell	3.23e-26	67
macrophage dendritic cell progenitor	4.93e-26	61
classical monocyte	1.44e-25	42
CD14-positive, CD16-negative classical monocyte	1.44e-25	42
monopoietic cell	2.53e-25	59
monocyte	2.53e-25	59
monoblast	2.53e-25	59
promonocyte	2.53e-25	59
myeloid lineage restricted progenitor cell	3.18e-25	66
myeloid leukocyte	6.18e-24	72
hematopoietic lineage restricted progenitor cell	3.01e-20	120
nongranular leukocyte	1.62e-19	115
leukocyte	9.16e-19	136
myeloid cell	3.97e-14	108
common myeloid progenitor	3.97e-14	108
hematopoietic cell	7.87e-14	177
hematopoietic stem cell	3.00e-13	168
angioblastic mesenchymal cell	3.00e-13	168
hematopoietic oligopotent progenitor cell	6.67e-13	161
hematopoietic multipotent progenitor cell	6.67e-13	161
stuff accumulating cell	5.99e-10	87

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.52e-27	98
blood island	1.52e-27	98
neural tube	1.70e-26	56
neural rod	1.70e-26	56
future spinal cord	1.70e-26	56
neural keel	1.70e-26	56
central nervous system	5.47e-26	81
hemolymphoid system	6.67e-26	108
bone marrow	1.68e-25	76
regional part of nervous system	9.82e-25	53
regional part of brain	9.82e-25	53
nervous system	9.98e-24	89
bone element	1.49e-23	82
immune system	1.56e-22	93
brain	1.88e-21	68
future brain	1.88e-21	68
skeletal element	6.21e-20	90
regional part of forebrain	8.12e-20	41
forebrain	8.12e-20	41
anterior neural tube	8.12e-20	41
future forebrain	8.12e-20	41
neural plate	3.73e-19	82
presumptive neural plate	3.73e-19	82
skeletal system	3.88e-19	100
neurectoderm	6.04e-19	86
brain grey matter	3.49e-18	34
gray matter	3.49e-18	34
telencephalon	4.15e-18	34
regional part of telencephalon	5.40e-17	32
cerebral hemisphere	7.21e-17	32
adult organism	6.64e-15	114
pre-chordal neural plate	8.39e-14	61
cerebral cortex	3.42e-13	25
pallium	3.42e-13	25
regional part of cerebral cortex	6.98e-13	22
neocortex	6.22e-12	20
ecto-epithelium	3.24e-10	104
structure with developmental contribution from neural crest	8.74e-10	132
posterior neural tube	7.54e-08	15
chordal neural plate	7.54e-08	15
musculoskeletal system	1.68e-07	167
ectoderm-derived structure	5.82e-07	171
ectoderm	5.82e-07	171
presumptive ectoderm	5.82e-07	171
segmental subdivision of nervous system	7.88e-07	13

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	3	18.2683513442277	0.000268166010572129	0.00286721846623081
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00997319412050402
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418978338106109
FOS#2353	4	8.9979553088944	0.000152514771116863	0.00194987026327262
GATA2#2624	3	9.5586988001655	0.00181815161835744	0.0109010813978778
GTF2B#2959	3	23.9578724507432	0.000119775456285592	0.00162457517909233
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0320105447644645
JUN#3725	3	9.38462189425225	0.00191899450203047	0.0112860607499471
JUNB#3726	3	22.9579744948659	0.000135977250401878	0.00177916913739937
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0386957862225173
RXRA#6256	2	10.0373085695666	0.0139170380592011	0.0488811682483573
STAT3#6774	3	7.88959874786568	0.00319076048168013	0.0167423550013159
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244420663072009
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0483074308252149
USF2#7392	3	9.7441480388022	0.00171834184841007	0.010721184318424

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.