Coexpression cluster:C1643

Full id: C1643_cerebellum_breast_pineal_spinal_acute_hippocampus_medulla

Phase1 CAGE Peaks

Hg19::chr11:71791726..71791756,-	p8@NUMA1
Hg19::chr1:150039659..150039684,-	p@chr1:150039659..150039684 -
Hg19::chr1:61547894..61547968,+	p2@NFIA
Hg19::chr1:61548069..61548102,+	p3@NFIA
Hg19::chr1:61548118..61548129,+	p9@NFIA

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:0051322	anaphase	0.0108906810524625
GO:0000090	mitotic anaphase	0.0108906810524625
GO:0005876	spindle microtubule	0.0197881225581302
GO:0019079	viral genome replication	0.0197881225581302
GO:0000922	spindle pole	0.0197881225581302
GO:0043025	cell soma	0.0197881225581302
GO:0006997	nuclear organization and biogenesis	0.0197881225581302
GO:0030425	dendrite	0.0197881225581302
GO:0016363	nuclear matrix	0.0197881225581302
GO:0008017	microtubule binding	0.0197881225581302
GO:0019058	viral infectious cycle	0.0197881225581302
GO:0022415	viral reproductive process	0.0206764560402455
GO:0015631	tubulin binding	0.0220289584636577
GO:0051321	meiotic cell cycle	0.0220289584636577
GO:0005819	spindle	0.0220289584636577
GO:0043005	neuron projection	0.0220289584636577

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.97e-51	114
neural tube	2.20e-31	56
neural rod	2.20e-31	56
future spinal cord	2.20e-31	56
neural keel	2.20e-31	56
organ system subdivision	2.63e-31	223
regional part of nervous system	1.69e-29	53
regional part of brain	1.69e-29	53
central nervous system	2.60e-29	81
nervous system	3.74e-29	89
brain	3.49e-27	68
future brain	3.49e-27	68
neurectoderm	2.38e-26	86
neural plate	9.80e-26	82
presumptive neural plate	9.80e-26	82
anatomical cluster	1.18e-24	373
regional part of forebrain	3.83e-24	41
forebrain	3.83e-24	41
anterior neural tube	3.83e-24	41
future forebrain	3.83e-24	41
ecto-epithelium	4.82e-21	104
ectoderm-derived structure	5.76e-21	171
ectoderm	5.76e-21	171
presumptive ectoderm	5.76e-21	171
brain grey matter	2.53e-20	34
gray matter	2.53e-20	34
telencephalon	3.11e-20	34
regional part of telencephalon	4.74e-19	32
cerebral hemisphere	6.66e-19	32
structure with developmental contribution from neural crest	3.41e-18	132
pre-chordal neural plate	7.04e-18	61
multi-tissue structure	7.20e-18	342
anatomical conduit	7.64e-17	240
cerebral cortex	5.28e-15	25
pallium	5.28e-15	25
tube	1.58e-14	192
regional part of cerebral cortex	1.92e-14	22
cell layer	2.36e-14	309
epithelium	3.04e-14	306
neocortex	2.64e-13	20
germ layer	7.25e-13	560
germ layer / neural crest	7.25e-13	560
embryonic tissue	7.25e-13	560
presumptive structure	7.25e-13	560
germ layer / neural crest derived structure	7.25e-13	560
epiblast (generic)	7.25e-13	560
embryonic structure	2.01e-12	564
developing anatomical structure	6.26e-12	581
multi-cellular organism	2.82e-11	656
embryo	1.17e-10	592
anatomical system	2.59e-09	624
anatomical group	4.95e-09	625
organ part	5.79e-09	218
posterior neural tube	2.29e-08	15
chordal neural plate	2.29e-08	15
subdivision of digestive tract	3.80e-08	118
organ	1.34e-07	503
digestive system	1.36e-07	145
digestive tract	1.36e-07	145
primitive gut	1.36e-07	145
segmental subdivision of nervous system	2.91e-07	13
endoderm-derived structure	6.78e-07	160
endoderm	6.78e-07	160
presumptive endoderm	6.78e-07	160
neural nucleus	8.55e-07	9
nucleus of brain	8.55e-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	0.0148892361857684
CHD2#1106	4	8.27521826729349	0.000402837356710173	0.00387652544894994
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00352222743345089
E2F4#1874	4	10.1344482522276	0.000181820150963297	0.00220265801490034
EGR1#1958	5	4.98817909481014	0.000323739800059071	0.00330444301977808
EP300#2033	4	5.41915338097856	0.0020938692794389	0.0121126406156707
FOXA1#3169	5	11.0814197493855	5.98116883436141e-06	0.000178731700112123
FOXA2#3170	3	14.7782782515991	0.000628919285119448	0.00517316698579113
HMGN3#9324	4	6.54283817868047	0.0010080127776835	0.00721858519531591
HNF4G#3174	2	11.5013690105787	0.0112743830492105	0.0413704339567315
NR2C2#7182	2	13.0458443620963	0.0088363641276826	0.0335439456648387
NR3C1#2908	4	11.9784186649384	9.4122920812787e-05	0.00136491304176155
SUZ12#23512	2	20.0463123644252	0.00382407565415475	0.0188726319461425
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135161670480681
ZBTB7A#51341	5	7.3519093078759	4.65425347594289e-05	0.000815306237460582

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.