Coexpression cluster:C3840

Full id: C3840_optic_cerebellum_Neutrophils_Eosinophils_occipital_skeletal_substantia

Phase1 CAGE Peaks

Hg19::chr1:10270620..10270637,+	p1@KIF1B
Hg19::chr1:10270675..10270686,+	p5@KIF1B
Hg19::chr5:147763388..147763474,-	p1@ENST00000501695 p1@uc003lpb.1

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:0008089	anterograde axon cargo transport	0.00476863299187566
GO:0008088	axon cargo transport	0.00476863299187566
GO:0019894	kinesin binding	0.00476863299187566
GO:0007274	neuromuscular synaptic transmission	0.00476863299187566
GO:0007270	nerve-nerve synaptic transmission	0.00805369127516778
GO:0030659	cytoplasmic vesicle membrane	0.029936418226775
GO:0044433	cytoplasmic vesicle part	0.029936418226775
GO:0012506	vesicle membrane	0.029936418226775
GO:0003777	microtubule motor activity	0.0332038149063935
GO:0007018	microtubule-based movement	0.0346167432002826
GO:0005875	microtubule associated complex	0.0346167432002826
GO:0030705	cytoskeleton-dependent intracellular transport	0.0346167432002826
GO:0007268	synaptic transmission	0.0414458966207465
GO:0005874	microtubule	0.0414458966207465
GO:0007017	microtubule-based process	0.0414458966207465
GO:0019226	transmission of nerve impulse	0.0414458966207465
GO:0016023	cytoplasmic membrane-bound vesicle	0.0414458966207465
GO:0031988	membrane-bound vesicle	0.0414458966207465
GO:0031410	cytoplasmic vesicle	0.0457788767220064
GO:0031982	vesicle	0.0457788767220064

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
classical monocyte	6.10e-16	42
CD14-positive, CD16-negative classical monocyte	6.10e-16	42
defensive cell	2.30e-15	48
phagocyte	2.30e-15	48
myeloid leukocyte	8.12e-14	72
macrophage dendritic cell progenitor	1.68e-13	61
monopoietic cell	1.08e-12	59
monocyte	1.08e-12	59
monoblast	1.08e-12	59
promonocyte	1.08e-12	59
granulocyte monocyte progenitor cell	1.27e-11	67
myeloid lineage restricted progenitor cell	2.62e-09	66
stuff accumulating cell	1.97e-07	87

Uber Anatomy

Ontology term	p-value	n
adult organism	1.51e-35	114
central nervous system	2.92e-31	81
neural tube	9.01e-30	56
neural rod	9.01e-30	56
future spinal cord	9.01e-30	56
neural keel	9.01e-30	56
nervous system	4.91e-29	89
regional part of nervous system	6.08e-28	53
regional part of brain	6.08e-28	53
brain	3.82e-27	68
future brain	3.82e-27	68
multi-cellular organism	2.69e-26	656
anatomical system	4.02e-26	624
anatomical group	6.66e-26	625
regional part of forebrain	4.46e-24	41
forebrain	4.46e-24	41
anterior neural tube	4.46e-24	41
future forebrain	4.46e-24	41
neural plate	1.30e-22	82
presumptive neural plate	1.30e-22	82
embryonic structure	5.19e-21	564
neurectoderm	8.63e-21	86
telencephalon	1.95e-20	34
brain grey matter	2.21e-20	34
gray matter	2.21e-20	34
germ layer	2.25e-20	560
germ layer / neural crest	2.25e-20	560
embryonic tissue	2.25e-20	560
presumptive structure	2.25e-20	560
germ layer / neural crest derived structure	2.25e-20	560
epiblast (generic)	2.25e-20	560
structure with developmental contribution from neural crest	2.36e-20	132
developing anatomical structure	3.49e-20	581
organ	1.08e-19	503
embryo	1.55e-19	592
regional part of telencephalon	3.64e-19	32
cerebral hemisphere	4.44e-19	32
ectoderm-derived structure	1.70e-17	171
ectoderm	1.70e-17	171
presumptive ectoderm	1.70e-17	171
pre-chordal neural plate	1.43e-16	61
organ system subdivision	8.01e-16	223
ecto-epithelium	8.94e-16	104
cerebral cortex	5.13e-15	25
pallium	5.13e-15	25
regional part of cerebral cortex	5.47e-14	22
neocortex	8.25e-13	20
anatomical cluster	8.06e-12	373
skeletal system	1.03e-10	100
bone element	1.29e-10	82
anatomical conduit	7.31e-10	240
bone marrow	1.33e-09	76
skeletal element	1.91e-09	90
tube	5.76e-09	192
immune system	1.04e-07	93
multi-tissue structure	1.13e-07	342
tissue	4.70e-07	773
hemolymphoid system	4.78e-07	108
posterior neural tube	5.34e-07	15
chordal neural plate	5.34e-07	15
hematopoietic system	5.67e-07	98
blood island	5.67e-07	98
basal ganglion	7.22e-07	9
nuclear complex of neuraxis	7.22e-07	9
aggregate regional part of brain	7.22e-07	9
collection of basal ganglia	7.22e-07	9
cerebral subcortex	7.22e-07	9
neural nucleus	7.65e-07	9
nucleus of brain	7.65e-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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279467161459726
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171755128420213
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325412207210582
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322233835482041
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462357434272725
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00897573271834518
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154123319754987
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128091719940431
IRF3#3661	2	31.3213014743264	0.00133951467332011	0.00887731283500726
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294537015868948
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174468294342853
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269639105221816
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0324789554116848
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381351524419455
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172925483525077
PBX3#5090	2	14.6096751244961	0.00605612247321789	0.0268359020314991
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00664075704032692
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276788185219753
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0329889512472795
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457474170725741
SP2#6668	2	17.4356869958964	0.00427356848176974	0.0203199280067175
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00543113809570494
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329416416112959
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140202329167744
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109416694934879

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.