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Coexpression cluster:C2695: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.0938548,MA0004.1;11.6425,MA0006.1;2.26728,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.896009,MA0017.1;1.41335,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;1.28333,MA0058.1;12.1276,MA0059.1;1.47051,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.841508,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;1.53734,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;15.9541,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;1.98562,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;1.43218,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;1.46638,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.481,MA0147.1;9.08203,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;15.8206,MA0138.2;3.52208,MA0002.2;0.98779,MA0137.2;0.558189,MA0104.2;7.08088,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;1.7213,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;13.242,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;2.15942,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;7.00686,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;5.32193,MA0442.1;0
}}
}}

Revision as of 20:50, 22 January 2013


Full id: C2695_neuroectodermal_Dendritic_thymus_acute_granulocyte_CD19_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr2:242824077..242824114,+p1@ENST00000429947
Hg19::chr2:242824118..242824127,+p4@ENST00000429947
Hg19::chr2:242824129..242824140,+p5@ENST00000429947
Hg19::chr2:242824142..242824158,+p2@ENST00000429947


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

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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
sympathetic nervous system5.30e-085
autonomic nervous system5.30e-085
Disease
Ontology termp-valuen
neuroectodermal tumor4.16e-1510
germ cell and embryonal cancer4.78e-0922
germ cell cancer4.78e-0922
neuroendocrine tumor4.98e-096


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)
MA0003.10.0938548
MA0004.111.6425
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.11.41335
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.28333
MA0058.112.1276
MA0059.11.47051
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.53734
MA0074.10.819248
MA0076.10.623864
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
MA0092.10.673508
MA0093.115.9541
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.98562
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.11.43218
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
MA0146.10.481
MA0147.19.08203
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.215.8206
MA0138.23.52208
MA0002.20.98779
MA0137.20.558189
MA0104.27.08088
MA0047.20.856092
MA0112.21.05083
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.113.242
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.27.00686
MA0102.21.75932
MA0258.10.418966
MA0259.15.32193
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
ATF3#467422.46317452600873.92475754624726e-060.000127495413179632
CCNT2#90546.336201576962630.0006203100587215640.00512982518194801
CHD2#1106410.34402283411698.73193255208051e-050.0012920860070937
CTCF#1066445.360256373075030.001211145381643620.00818551818504357
EBF1#187948.9064668465690.00015887907472010.00199845497828406
EGR1#195844.988179094810140.001615011500076050.0101565716900369
ELF1#199744.258097958807540.003041525565781240.0161139293138856
ETS1#211349.728760922202340.0001115955317418140.00154677183007077
FOSL1#8061329.78518478727986.26173959487248e-050.00102519175662155
GABPB1#255347.067683836182170.0004006876864423170.00390659272632087
HDAC2#3066413.41562023662633.0859005065161e-050.00062763069717631
HMGN3#932448.178547723350590.0002234570284440470.00248404774812856
IRF1#365947.63716375356390.0002938853996185490.0030788541730125
MAX#414946.452555509007120.0005767613195645490.00485894776591126
MXI1#460149.96157162875930.0001015224754950450.00142569662743404
MYC#460945.22228187160940.001344309395272740.00888597018562591
NFE2#4778477.2042606516292.80776035215453e-081.91785273655112e-06
NFKB1#479045.488063424193840.001102199566301980.00768544668881108
PAX5#507946.669565531177830.0005052774169483260.00444496867829062
SIN3A#2594245.408884726815140.001168172384885160.00797351517580686
SP1#666745.69838137814090.0009482606065333980.00685034166740967
SPI1#668836.153242631392040.006580387113059030.0281071960124646
STAT1#6772420.70658749719925.43610708103893e-060.000165522328698724
TCF7L2#6934410.77017656313737.42969445082454e-050.00115589134328864
TRIM28#10155418.59052504526258.36730015875654e-060.000230573208781102
USF1#739146.361499277207960.0006105011399140830.00508535081763335
USF2#7392412.99219738506963.50833029870167e-050.000681940271852044
ZBTB7A#5134135.513931980906920.009038352821081090.0342534483736442
ZEB1#6935416.88843201754391.22862303393937e-050.000304861394729375
ZNF143#7702413.50087655222793.00867915035614e-050.000621486237705785



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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