Coexpression cluster:C3723

Full id: C3723_nonsmall_globus_spinal_medulla_thalamus_pineal_brain

Phase1 CAGE Peaks

Hg19::chr18:47013532..47013544,-	p3@C18orf32
Hg19::chr18:47013564..47013585,-	p2@C18orf32
Hg19::chr18:47013586..47013633,-	p1@C18orf32

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
myeloid leukocyte	1.98e-20	76
granulocyte monocyte progenitor cell	2.92e-16	71
CD14-positive, CD16-negative classical monocyte	4.84e-16	42
macrophage dendritic cell progenitor	2.55e-15	65
myeloid lineage restricted progenitor cell	4.07e-15	70
monopoietic cell	1.23e-14	63
monocyte	1.23e-14	63
monoblast	1.23e-14	63
promonocyte	1.23e-14	63
leukocyte	2.04e-13	140
classical monocyte	4.47e-13	45
hematopoietic lineage restricted progenitor cell	2.29e-09	124
nongranular leukocyte	3.38e-08	119

Uber Anatomy

Ontology term	p-value	n
neural tube	1.35e-28	57
neural rod	1.35e-28	57
future spinal cord	1.35e-28	57
neural keel	1.35e-28	57
regional part of brain	1.50e-24	59
central nervous system	8.72e-23	82
anterior neural tube	2.23e-22	42
regional part of forebrain	5.01e-22	41
forebrain	5.01e-22	41
future forebrain	5.01e-22	41
adult organism	1.04e-21	115
neural plate	2.55e-21	86
presumptive neural plate	2.55e-21	86
regional part of nervous system	6.43e-21	94
nervous system	6.43e-21	94
brain	1.40e-20	69
future brain	1.40e-20	69
neurectoderm	6.64e-20	90
gray matter	3.65e-18	34
brain grey matter	3.65e-18	34
telencephalon	4.98e-18	34
regional part of telencephalon	1.77e-17	33
cerebral hemisphere	7.01e-17	32
pre-chordal neural plate	8.64e-16	61
bone marrow	1.48e-13	80
regional part of cerebral cortex	2.06e-13	22
cerebral cortex	5.69e-13	25
pallium	5.69e-13	25
neocortex	3.26e-12	20
bone element	1.92e-11	86
hematopoietic system	6.30e-11	102
blood island	6.30e-11	102
skeletal element	8.34e-10	101
skeletal system	8.34e-10	101
hemolymphoid system	1.04e-09	112
tube	2.43e-09	194
head	3.11e-09	123
immune system	6.97e-09	115
anterior region of body	1.50e-08	129
craniocervical region	1.50e-08	129
posterior neural tube	2.11e-07	15
chordal neural plate	2.11e-07	15
ectoderm-derived structure	3.60e-07	169
ectoderm	8.37e-07	173
presumptive ectoderm	8.37e-07	173
nucleus of brain	9.98e-07	9
neural nucleus	9.98e-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
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139149252946022
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189916544682295
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115185542942615
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00660185228094452
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325124856941144
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321995431881163
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00914751219942148
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462010010830071
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255657649265593
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.0058103359005598
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.01540270127441
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108651688583692
JUND#3727	3	6.99466394187103	0.00292184504273499	0.015668236517673
MAX#4149	3	6.45255550900712	0.00372191383426551	0.018639731415405
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294324208648395
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000737398304986264
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269478092320426
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245698320969458
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000604919280665343
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470933492110122
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172832083725471
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00881811442699286
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00663841329887131
REST#5978	3	9.65002871612802	0.00111263624711459	0.00767064605006275
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276533027454203
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246327016674283
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000939578071370626
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00542565550560988
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00629079939148467
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00613418649364031
USF1#7391	3	6.36149927720796	0.0038840405729056	0.019016704017331
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329182717662278
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140105158496572
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242652835731305
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109353013934451

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.