Coexpression cluster:C2551

Full id: C2551_nonsmall_neuroblastoma_retinoblastoma_carcinoid_Reticulocytes_non_mesothelioma

Phase1 CAGE Peaks

Hg19::chr1:202311054..202311071,-	p1@UBE2T
Hg19::chr1:202311079..202311086,-	p3@UBE2T
Hg19::chr1:202311088..202311099,-	p2@UBE2T
Hg19::chr1:203830938..203831001,+	p3@SNRPE

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:0030532	small nuclear ribonucleoprotein complex	0.0452854120733943
GO:0000245	spliceosome assembly	0.0452854120733943
GO:0000375	RNA splicing, via transesterification reactions	0.0452854120733943
GO:0000398	nuclear mRNA splicing, via spliceosome	0.0452854120733943
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0452854120733943

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	1.67e-17	253
animal cell	1.66e-16	679
eukaryotic cell	1.66e-16	679
embryonic cell	4.22e-10	250
migratory neural crest cell	4.62e-10	41
neurectodermal cell	3.27e-09	59
neural cell	3.89e-09	25
native cell	5.20e-09	722
ectodermal cell	1.12e-07	72
neuron associated cell	1.69e-07	17
neuron associated cell (sensu Vertebrata)	1.69e-07	17
non-terminally differentiated cell	7.21e-07	106

Uber Anatomy

Ontology term	p-value	n
larynx	5.30e-07	9

Disease

Ontology term	p-value	n
cancer	4.96e-49	235
disease of cellular proliferation	1.53e-48	239
organ system cancer	1.85e-24	137
cell type cancer	6.79e-24	143
carcinoma	5.83e-19	106
hematologic cancer	3.25e-17	51
immune system cancer	3.25e-17	51
leukemia	4.13e-14	39
myeloid leukemia	8.41e-11	31

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
CEBPB#1051	4	7.97114762582482	0.000247638578809083	0.00268206217279288
CHD2#1106	3	7.75801712558764	0.00335152246453634	0.0172990834572359
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106522611950842
E2F4#1874	4	12.6680603152844	3.88145892637771e-05	0.000727000876635513
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00997198722341193
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160959659774323
FOS#2353	3	6.7484664816708	0.00503245277631794	0.0234677770809908
GTF2F1#2962	4	12.7396608767577	3.79492332235515e-05	0.000718654572735177
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186170993517037
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00307669379017258
IRF3#3661	3	35.2364641586172	3.79279212646878e-05	0.000719948049611547
JUN#3725	3	9.38462189425225	0.00191899450203047	0.0112854252377702
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00391830791563412
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00485581422442579
MXI1#4601	4	9.9615716287593	0.000101522475495045	0.0014245473355135
MYC#4609	4	5.2222818716094	0.00134430939527274	0.0088803497111252
NANOG#79923	4	29.2447784810127	1.36586687657858e-06	5.33469598814475e-05
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00768134395469186
NFYA#4800	3	13.8191855248729	0.000613241180673451	0.00508788494346636
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.00618957746999076
NR2C2#7182	4	32.6146109052409	8.82887529809196e-07	3.8212967561435e-05
NRF1#4899	3	9.15770958578318	0.00206195379173342	0.0119631349399948
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00444048032216982
POU2F2#5452	4	9.10612405774252	0.00014539566517493	0.00188445990012465
REST#5978	3	7.23752153709602	0.00410469730419261	0.0195820611069145
RFX5#5993	4	12.0479108271951	4.74457429336527e-05	0.000827104981847397
RXRA#6256	4	20.0746171391333	6.1537798808435e-06	0.000182324714035578
SETDB1#9869	3	30.2400196335079	5.98509618524166e-05	0.000984839231905551
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00796726674753613
SP1#6667	4	5.6983813781409	0.000948260606533398	0.0068456065172974
SREBF1#6720	3	35.2543870803662	3.78704019553645e-05	0.000725049845979158
SRF#6722	3	10.3478836966259	0.00143989377840126	0.00923886873026045
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322421578110251
TAF7#6879	4	11.4330694049239	5.85061525419808e-05	0.000969738781992054
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244388266589318
TCF7L2#6934	3	8.07763242235301	0.00297838168583462	0.0158655108072468
TFAP2A#7020	4	16.518634373045	1.34240829060362e-05	0.00032657763676299
TFAP2C#7022	4	10.8092286098602	7.32289634782688e-05	0.00114559013132219
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106896872883945
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00346769033625012
ZEB1#6935	4	16.8884320175439	1.22862303393937e-05	0.00030428304728858

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.