Coexpression cluster:C3751

Full id: C3751_Mesenchymal_Renal_Reticulocytes_Alveolar_neuroblastoma_nonsmall_Neurons

Phase1 CAGE Peaks

Hg19::chr19:12912626..12912647,-	p3@PRDX2
Hg19::chr19:12912657..12912669,-	p2@PRDX2
Hg19::chr19:12912688..12912699,-	p4@PRDX2

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
electrically responsive cell	4.75e-14	60
electrically active cell	4.75e-14	60
embryonic cell	5.12e-14	248
contractile cell	2.92e-13	59
mesodermal cell	1.61e-12	119
smooth muscle cell	1.32e-11	42
smooth muscle myoblast	1.32e-11	42
muscle cell	4.35e-11	54
muscle precursor cell	1.98e-10	57
myoblast	1.98e-10	57
multi-potent skeletal muscle stem cell	1.98e-10	57
non-terminally differentiated cell	3.00e-10	180
vascular associated smooth muscle cell	9.76e-10	32
ectodermal cell	8.99e-09	71
neurectodermal cell	4.13e-08	59
stuff accumulating cell	1.41e-07	39

Uber Anatomy

Ontology term	p-value	n
epithelium	9.65e-23	309
cell layer	1.54e-22	312
anatomical cluster	5.98e-18	286
multi-tissue structure	2.54e-17	347
tube	5.28e-16	194
anatomical conduit	5.24e-15	241
vasculature	2.75e-14	79
vascular system	2.75e-14	79
organism subdivision	9.53e-14	365
epithelial tube	3.48e-13	118
organ part	1.34e-12	219
splanchnic layer of lateral plate mesoderm	2.96e-12	84
vessel	1.10e-11	69
circulatory system	2.06e-11	113
skeletal muscle tissue	5.09e-11	61
striated muscle tissue	5.09e-11	61
myotome	5.09e-11	61
dermomyotome	6.43e-11	70
multilaminar epithelium	7.43e-11	82
ectoderm-derived structure	7.77e-11	169
ectoderm	7.99e-11	173
presumptive ectoderm	7.99e-11	173
trunk mesenchyme	9.08e-11	143
blood vessel	1.31e-10	60
epithelial tube open at both ends	1.31e-10	60
blood vasculature	1.31e-10	60
vascular cord	1.31e-10	60
somite	1.71e-10	83
paraxial mesoderm	1.71e-10	83
presomitic mesoderm	1.71e-10	83
presumptive segmental plate	1.71e-10	83
trunk paraxial mesoderm	1.71e-10	83
presumptive paraxial mesoderm	1.71e-10	83
cardiovascular system	1.98e-10	110
neural plate	2.36e-10	86
presumptive neural plate	2.36e-10	86
pre-chordal neural plate	2.64e-10	61
muscle tissue	2.72e-10	63
musculature	2.72e-10	63
musculature of body	2.72e-10	63
neurectoderm	3.36e-10	90
regional part of nervous system	6.46e-10	94
nervous system	6.46e-10	94
unilaminar epithelium	1.88e-09	138
multi-cellular organism	3.26e-09	659
artery	6.12e-09	42
arterial blood vessel	6.12e-09	42
arterial system	6.12e-09	42
central nervous system	7.43e-09	82
compound organ	7.92e-09	69
head	3.46e-08	123
eye	1.63e-07	20
camera-type eye	1.94e-07	19
simple eye	1.94e-07	19
ocular region	1.94e-07	19
optic cup	1.94e-07	19
eye primordium	1.94e-07	19
optic vesicle	1.94e-07	19
anterior region of body	2.82e-07	129
craniocervical region	2.82e-07	129
embryo	3.25e-07	612
face	3.29e-07	21
sense organ	4.48e-07	23
trunk	6.81e-07	216
visual system	8.37e-07	21

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
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164167313035828
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189951694884902
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279375045877687
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322083223733744
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320513318825304
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462104710886951
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167423024144287
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.005811215921143
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00433714703220061
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108664058560192
JUND#3727	3	6.99466394187103	0.00292184504273499	0.015671455136514
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186424132625224
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00720088424393667
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294383290912858
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.00073752861039446
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269547074297213
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.017284905800201
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00881923911475856
REST#5978	3	9.65002871612802	0.00111263624711459	0.00767216539102077
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00484386679847972
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165205378724927
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027660256926923
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239640576365512
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246370028201553
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00542734127708902
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00629216705567587
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00613508699077678
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190184871955407
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329244185100315
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.014012009906266
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.002426800024169
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109378477437521

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.