Coexpression cluster:C1680

Full id: C1680_Neutrophils_Eosinophils_pineal_optic_cerebellum_pituitary_parietal

Phase1 CAGE Peaks

Hg19::chr12:62860581..62860620,+	p1@MON2
Hg19::chr1:12290063..12290118,+	p1@VPS13D
Hg19::chr4:123073464..123073547,+	p1@KIAA1109
Hg19::chr6:38607673..38607749,-	p1@BTBD9
Hg19::chr8:9413410..9413451,+	p1@TNKS

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:0008104	protein localization	0.0113683186556758
GO:0033036	macromolecule localization	0.0113683186556758
GO:0018107	peptidyl-threonine phosphorylation	0.0113683186556758
GO:0018210	peptidyl-threonine modification	0.0113683186556758
GO:0006895	Golgi to endosome transport	0.0170257968800675
GO:0000139	Golgi membrane	0.0170257968800675
GO:0018209	peptidyl-serine modification	0.0170257968800675
GO:0018105	peptidyl-serine phosphorylation	0.0170257968800675
GO:0044431	Golgi apparatus part	0.0170257968800675
GO:0007004	telomere maintenance via telomerase	0.0257469581026292
GO:0006892	post-Golgi vesicle-mediated transport	0.0289068878369803
GO:0005794	Golgi apparatus	0.0312744347931803
GO:0032200	telomere organization and biogenesis	0.0312744347931803
GO:0000723	telomere maintenance	0.0312744347931803
GO:0000781	chromosome, telomeric region	0.0312744347931803
GO:0003950	NAD+ ADP-ribosyltransferase activity	0.0352887257354325
GO:0016197	endosome transport	0.0352887257354325
GO:0015031	protein transport	0.0352887257354325
GO:0046907	intracellular transport	0.035882627027328
GO:0045184	establishment of protein localization	0.035882627027328
GO:0012505	endomembrane system	0.0408007570046309
GO:0006278	RNA-dependent DNA replication	0.0408007570046309
GO:0051649	establishment of cellular localization	0.0408007570046309
GO:0065002	intracellular protein transport across a membrane	0.0408007570046309
GO:0051641	cellular localization	0.0408007570046309
GO:0016763	transferase activity, transferring pentosyl groups	0.0408007570046309
GO:0051028	mRNA transport	0.0408007570046309
GO:0004190	aspartic-type endopeptidase activity	0.0408007570046309
GO:0005643	nuclear pore	0.0408007570046309
GO:0048193	Golgi vesicle transport	0.0408007570046309
GO:0050658	RNA transport	0.0408007570046309
GO:0051236	establishment of RNA localization	0.0408007570046309
GO:0050657	nucleic acid transport	0.0408007570046309
GO:0006403	RNA localization	0.0408007570046309
GO:0046930	pore complex	0.0417767984157967
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0435294639387703
GO:0044453	nuclear membrane part	0.0451850483065894
GO:0018193	peptidyl-amino acid modification	0.0477275083872672
GO:0031090	organelle membrane	0.0477275083872672
GO:0051179	localization	0.0479964255474786

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	2.36e-11	140
myeloid leukocyte	5.04e-09	76
CD14-positive, CD16-negative classical monocyte	8.78e-08	42
hematopoietic lineage restricted progenitor cell	2.43e-07	124
nongranular leukocyte	4.02e-07	119
granulocyte monocyte progenitor cell	5.32e-07	71
hematopoietic stem cell	5.43e-07	172
angioblastic mesenchymal cell	5.43e-07	172

Uber Anatomy

Ontology term	p-value	n
adult organism	3.04e-45	115
neural tube	1.72e-27	57
neural rod	1.72e-27	57
future spinal cord	1.72e-27	57
neural keel	1.72e-27	57
regional part of brain	7.32e-25	59
anterior neural tube	2.51e-24	42
regional part of forebrain	4.21e-24	41
forebrain	4.21e-24	41
future forebrain	4.21e-24	41
central nervous system	4.83e-24	82
brain	1.90e-23	69
future brain	1.90e-23	69
regional part of nervous system	5.64e-22	94
nervous system	5.64e-22	94
telencephalon	8.34e-20	34
gray matter	9.66e-20	34
brain grey matter	9.66e-20	34
regional part of telencephalon	3.37e-19	33
cerebral hemisphere	1.22e-18	32
neurectoderm	4.15e-17	90
neural plate	1.41e-16	86
presumptive neural plate	1.41e-16	86
regional part of cerebral cortex	4.28e-15	22
cerebral cortex	1.81e-14	25
pallium	1.81e-14	25
neocortex	7.98e-14	20
anterior region of body	3.75e-13	129
craniocervical region	3.75e-13	129
pre-chordal neural plate	1.38e-12	61
head	4.13e-12	123
ectoderm	4.45e-11	173
presumptive ectoderm	4.45e-11	173
ectoderm-derived structure	1.44e-10	169
hematopoietic system	4.61e-07	102
blood island	4.61e-07	102
basal ganglion	8.88e-07	9
nuclear complex of neuraxis	8.88e-07	9
aggregate regional part of brain	8.88e-07	9
collection of basal ganglia	8.88e-07	9
cerebral subcortex	8.88e-07	9
nucleus of brain	9.29e-07	9
neural nucleus	9.29e-07	9

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
CCNT2#905	4	5.06896126157011	0.00270999809128077	0.0148915863756326
E2F1#1869	4	3.92591137190346	0.00721498454710636	0.0298698129430864
E2F6#1876	5	5.01715573169739	0.000314497859929779	0.00322555651509439
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.00572747913677329
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00673740145466063
IRF1#3659	4	6.10973100285112	0.00131552526476799	0.00880775326156192
MXI1#4601	3	5.97694297725558	0.00865300488936688	0.0329460874094272
NANOG#79923	2	11.6979113924051	0.0109116495195608	0.0402160343075629
NFKB1#4790	5	5.48806342419384	0.000200816284746232	0.00238845825789906
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00247844382752982
SIX5#147912	4	13.6693722843672	5.58844770365977e-05	0.0009374428039231
SRF#6722	4	11.0377426097342	0.000129925581484675	0.00171005643411191
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135220134571724
THAP1#55145	2	12.5476578411405	0.00952843466738653	0.0358893605102128

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.