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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.117089601335341,0

Latest revision as of 11:44, 17 September 2013


Full id: C1426_CD14_bile_mucinous_lung_large_glioblastoma_nonsmall



Phase1 CAGE Peaks

Hg19::chr16:83986837..83986852,+p1@OSGIN1
Hg19::chr1:94374914..94374922,-p7@GCLM
Hg19::chr1:94374946..94374994,-p1@GCLM
Hg19::chr20:633833..633851,-p1@SRXN1
Hg19::chr4:139092367..139092379,-p@chr4:139092367..139092379
-
Hg19::chr4:139163058..139163082,-p8@SLC7A11


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:0006979response to oxidative stress0.00267447141343291
GO:0035226glutamate-cysteine ligase catalytic subunit binding0.00267447141343291
GO:0015327cystine:glutamate antiporter activity0.00267447141343291
GO:0035229positive regulation of glutamate-cysteine ligase activity0.00267447141343291
GO:0032542sulfiredoxin activity0.00267447141343291
GO:0035227regulation of glutamate-cysteine ligase activity0.00267447141343291
GO:0051409response to nitrosative stress0.00267447141343291
GO:0017109glutamate-cysteine ligase complex0.00416010516649996
GO:0004357glutamate-cysteine ligase activity0.00416010516649996
GO:0005294neutral L-amino acid secondary active transmembrane transporter activity0.00534823430200747
GO:0015184L-cystine transmembrane transporter activity0.00534823430200747
GO:0051900regulation of mitochondrial depolarization0.00534823430200747
GO:0000099sulfur amino acid transmembrane transporter activity0.00534823430200747
GO:0051351positive regulation of ligase activity0.00534823430200747
GO:0051882mitochondrial depolarization0.00623933116986053
GO:0051340regulation of ligase activity0.00660605893926391
GO:0006534cysteine metabolic process0.00660605893926391
GO:0005313L-glutamate transmembrane transporter activity0.0078802164471195
GO:0006750glutathione biosynthetic process0.0078802164471195
GO:0015172acidic amino acid transmembrane transporter activity0.00802058041895813
GO:0051899membrane depolarization0.00802058041895813
GO:0051881regulation of mitochondrial membrane potential0.00894971234644914
GO:0043524negative regulation of neuron apoptosis0.00894971234644914
GO:0005829cytosol0.0108478504797685
GO:0042221response to chemical stimulus0.0111896010626077
GO:0006536glutamate metabolic process0.0115131714638974
GO:0015175neutral amino acid transmembrane transporter activity0.0117791598889394
GO:0006749glutathione metabolic process0.0126936457064729
GO:0043523regulation of neuron apoptosis0.0161219563560019
GO:0016667oxidoreductase activity, acting on sulfur group of donors0.0169452130303383
GO:0005275amine transmembrane transporter activity0.0169452130303383
GO:0000096sulfur amino acid metabolic process0.0169452130303383
GO:0051402neuron apoptosis0.0169975821508008
GO:0042391regulation of membrane potential0.0170468221915915
GO:0015179L-amino acid transmembrane transporter activity0.0170932013623182
GO:0065008regulation of biological quality0.0200632651173214
GO:0035150regulation of tube size0.0206031839965857
GO:0050880regulation of blood vessel size0.0206031839965857
GO:0003018vascular process in circulatory system0.0206031839965857
GO:0044272sulfur compound biosynthetic process0.0210205779842032
GO:0009653anatomical structure morphogenesis0.0211854925063784
GO:0015300solute:solute antiporter activity0.0223308459100891
GO:0030308negative regulation of cell growth0.0223308459100891
GO:0045792negative regulation of cell size0.0223308459100891
GO:0048523negative regulation of cellular process0.0223308459100891
GO:0009069serine family amino acid metabolic process0.0223308459100891
GO:0048519negative regulation of biological process0.0230630761274883
GO:0045926negative regulation of growth0.0230630761274883
GO:0006950response to stress0.0230630761274883
GO:0015171amino acid transmembrane transporter activity0.0230630761274883
GO:0042493response to drug0.0230630761274883
GO:0006865amino acid transport0.0251250696915076
GO:0009064glutamine family amino acid metabolic process0.0284879107806133
GO:0035239tube morphogenesis0.0284879107806133
GO:0015837amine transport0.0284879107806133
GO:0006790sulfur metabolic process0.0286428388044346
GO:0015297antiporter activity0.029769822580319
GO:0046943carboxylic acid transmembrane transporter activity0.0302525219420084
GO:0046942carboxylic acid transport0.0302525219420084
GO:0015849organic acid transport0.0302525219420084
GO:0005342organic acid transmembrane transporter activity0.0302525219420084
GO:0016491oxidoreductase activity0.0303262360818528
GO:0046982protein heterodimerization activity0.0310591708125885
GO:0035295tube development0.0340499713122673
GO:0048869cellular developmental process0.0381580052831729
GO:0030154cell differentiation0.0381580052831729
GO:0008015blood circulation0.0436428645669278
GO:0003013circulatory system process0.0436428645669278
GO:0001558regulation of cell growth0.0436428645669278
GO:0048856anatomical structure development0.0438016778475504



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>

Uber Anatomy
Ontology termp-valuen
musculoskeletal system2.05e-13167
anatomical system2.83e-13624
anatomical group4.31e-13625
multi-cellular organism1.02e-12656
mesoderm7.51e-12315
mesoderm-derived structure7.51e-12315
presumptive mesoderm7.51e-12315
trunk7.44e-10199
skeletal system2.32e-09100
epithelial tube2.91e-09117
organism subdivision3.20e-09264
skeletal element3.74e-0990
bone marrow1.55e-0876
unilaminar epithelium3.42e-08148
bone element3.65e-0882
artery4.21e-0842
arterial blood vessel4.21e-0842
arterial system4.21e-0842
organ1.27e-07503
lateral plate mesoderm1.27e-07203
developing anatomical structure1.73e-07581
vessel6.17e-0768
embryo6.28e-07592
mesenchyme8.71e-07160
entire embryonic mesenchyme8.71e-07160


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)
MA0003.14.08206
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.11.149
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0569999
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.11.34409
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.12.32368
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.86787
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.13.11622
MA0145.10.707171
MA0146.11.8938
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.569061
MA0138.20.765223
MA0002.20.255126
MA0137.21.06611
MA0104.21.35181
MA0047.20.695777
MA0112.20.680553
MA0065.22.35074
MA0150.12.10974
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.11.09123
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.11.57484
MA0160.10.600559
MA0161.10
MA0162.10.347838
MA0163.11.18186
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.21.68161
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
BCLAF1#9774310.82632380506090.001772351046991060.0108896676665902
CCNT2#90544.224134384641760.007109805478875810.0296116196525886
CTCF#1066443.573504248716680.01316635007238510.0466049969567812
CTCFL#14069039.873237179487180.002312760027857710.0131187456305361
E2F1#186954.089491012399440.001749817597761990.0107588131456885
E2F4#187436.334030157642220.008197175368374340.0323620170219115
E2F6#187654.180963109747820.001573598759586970.0099748167548254
EGR1#195854.156815912341780.001617966818864440.010133663364041
ELF1#199753.548414965672950.003446837775721690.0175311332647608
FOS#235345.998636872596270.001899823711886350.0111840194265091
FOSL1#8061319.85678985818650.0003014027572522190.00311049432457159
GTF2B#2959315.97191496716210.0005711653715892990.00486716222612719
HDAC2#306648.94374682441750.0004094079565307180.00390307234797915
HEY1#2346253.366759202588090.004423827045203030.0209504408821457
HNF4A#3172311.56614518147680.001463487150085730.00937700211458919
JUN#372536.256414596168170.008486346850954870.0324143502456525
JUND#372744.663109294580680.004917643408260230.0229919312344566
MAFF#23764437.54357099329681.44675523683818e-065.6232850829975e-05
MAFK#7975418.06715542521992.61700332070418e-050.000564238666001288
NFE2#4778338.60213032581454.21574363639564e-050.000754822646393835
REST#597846.433352477418680.001454954223032070.00932518957344256
SIN3A#2594254.507403939012610.001096110061208640.00766088728384988
SMC3#912637.522466422466420.005039540716828550.0234819573893485
STAT1#6772310.35329374859960.002016680459920930.0117219551732904
STAT2#6773221.75459039548020.003379142399893220.0172557330873483
STAT3#677435.259732498577120.01377662058078550.048471111603445
TAF1#687252.785871904787740.01078636340290410.039792193833836
TAF7#687935.716534702461960.01092729379889660.04021267220095
TBP#690853.088975572580320.006645448275786930.0282879141012803
TCF7L2#693447.180117708758230.0009553297120679730.00687572736535504



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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