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{{Coexpression_clusters
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|full_id=C2551_nonsmall_neuroblastoma_retinoblastoma_carcinoid_Reticulocytes_non_mesothelioma
|gostat_on_coexpression_clusters=GO:0030532!small nuclear ribonucleoprotein complex!0.0452854120733943!6635$GO:0000245!spliceosome assembly!0.0452854120733943!6635$GO:0000375!RNA splicing, via transesterification reactions!0.0452854120733943!6635$GO:0000398!nuclear mRNA splicing, via spliceosome!0.0452854120733943!6635$GO:0000377!RNA splicing, via transesterification reactions with bulged adenosine as nucleophile!0.0452854120733943!6635
|id=C2551
}}

Latest revision as of 12:08, 17 September 2013


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

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

GO IDGO nameFDR corrected p-value
GO:0030532small nuclear ribonucleoprotein complex0.0452854120733943
GO:0000245spliceosome assembly0.0452854120733943
GO:0000375RNA splicing, via transesterification reactions0.0452854120733943
GO:0000398nuclear mRNA splicing, via spliceosome0.0452854120733943
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0452854120733943



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>

Cell Type
Ontology termp-valuen
epithelial cell1.67e-17253
animal cell1.66e-16679
eukaryotic cell1.66e-16679
embryonic cell4.22e-10250
migratory neural crest cell4.62e-1041
neurectodermal cell3.27e-0959
neural cell3.89e-0925
native cell5.20e-09722
ectodermal cell1.12e-0772
neuron associated cell1.69e-0717
neuron associated cell (sensu Vertebrata)1.69e-0717
non-terminally differentiated cell7.21e-07106
Uber Anatomy
Ontology termp-valuen
larynx5.30e-079
Disease
Ontology termp-valuen
cancer4.96e-49235
disease of cellular proliferation1.53e-48239
organ system cancer1.85e-24137
cell type cancer6.79e-24143
carcinoma5.83e-19106
hematologic cancer3.25e-1751
immune system cancer3.25e-1751
leukemia4.13e-1439
myeloid leukemia8.41e-1131


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

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.443649
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.12.70115
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.11.91637
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.12.72365
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.12.66544
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.11.78721
MA0161.10
MA0162.10.640035
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.00910927
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105147.971147625824820.0002476385788090830.00268206217279288
CHD2#110637.758017125587640.003351522464536340.0172990834572359
E2F1#186944.907389214879320.001724022357361790.0106522611950842
E2F4#1874412.66806031528443.88145892637771e-050.000727000876635513
E2F6#187645.017155731697390.00157802193473060.00997198722341193
ELF1#199744.258097958807540.003041525565781240.0160959659774323
FOS#235336.74846648167080.005032452776317940.0234677770809908
GTF2F1#2962412.73966087675773.79492332235515e-050.000718654572735177
HEY1#2346244.040111043105710.00375304636917980.0186170993517037
IRF1#365947.63716375356390.0002938853996185490.00307669379017258
IRF3#3661335.23646415861723.79279212646878e-050.000719948049611547
JUN#372539.384621894252250.001918994502030470.0112854252377702
JUND#372746.994663941871030.000417684217818580.00391830791563412
MAX#414946.452555509007120.0005767613195645490.00485581422442579
MXI1#460149.96157162875930.0001015224754950450.0014245473355135
MYC#460945.22228187160940.001344309395272740.0088803497111252
NANOG#79923429.24477848101271.36586687657858e-065.33469598814475e-05
NFKB1#479045.488063424193840.001102199566301980.00768134395469186
NFYA#4800313.81918552487290.0006132411806734510.00508788494346636
NFYB#4801312.56984494015230.000811456397697350.00618957746999076
NR2C2#7182432.61461090524098.82887529809196e-073.8212967561435e-05
NRF1#489939.157709585783180.002061953791733420.0119631349399948
PAX5#507946.669565531177830.0005052774169483260.00444048032216982
POU2F2#545249.106124057742520.000145395665174930.00188445990012465
REST#597837.237521537096020.004104697304192610.0195820611069145
RFX5#5993412.04791082719514.74457429336527e-050.000827104981847397
RXRA#6256420.07461713913336.1537798808435e-060.000182324714035578
SETDB1#9869330.24001963350795.98509618524166e-050.000984839231905551
SIN3A#2594245.408884726815140.001168172384885160.00796726674753613
SP1#666745.69838137814090.0009482606065333980.0068456065172974
SREBF1#6720335.25438708036623.78704019553645e-050.000725049845979158
SRF#6722310.34788369662590.001439893778401260.00923886873026045
TAF1#687243.343046285745290.008005664898701650.0322421578110251
TAF7#6879411.43306940492395.85061525419808e-050.000969738781992054
TBP#690843.706770687096390.005296377814784350.0244388266589318
TCF7L2#693438.077632422353010.002978381685834620.0158655108072468
TFAP2A#7020416.5186343730451.34240829060362e-050.00032657763676299
TFAP2C#7022410.80922860986027.32289634782688e-050.00114559013132219
YY1#752844.911170749853860.00171871838055440.0106896872883945
ZBTB7A#5134147.35190930787590.000342223540015990.00346769033625012
ZEB1#6935416.88843201754391.22862303393937e-050.00030428304728858



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

This analysis result is provided for C0 - C305 clusters.

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