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Coexpression cluster:C3503: Difference between revisions

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{{Coexpression_clusters
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0995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.0363723,0.150733,0.0254879,0.123917,0.184317,0.185335,0.0723291,0.258496,0.0377094,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.0541163,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,3.46304,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,2.1336,0.63186,1.91835,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,1.95727,3.26509,0.635379,1.7611,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,2.48753,0.137917,1.45286,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.901413,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,2.16722,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,4.3166,1.45054,5.03292,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,1.55552,1.48681,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,2.55998,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,6.79118,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,2.2314,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,1.96632,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,2.48899,0.883164,1.08214,2.31409,0.773313,1.33389,0.318511,7.72083,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;2.61626,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;1.88666,MA0009.1;1.3275,MA0014.1;0.758317,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;2.67616,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0185922,MA0074.1;0.935474,MA0076.1;1.74184,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;1.31954,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;1.80901,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;2.91906,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;1.37817,MA0146.1;0.707589,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.9924,MA0035.2;0.894194,MA0039.2;1.62945,MA0138.2;1.04628,MA0002.2;1.20011,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;1.31345,MA0156.1;1.60572,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.941469,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3503_osteoclastoma_acute_small_hepatoblastoma_stomach_sacrococcigeal_heart
|id=C3503
}}

Latest revision as of 12:27, 17 September 2013


Full id: C3503_osteoclastoma_acute_small_hepatoblastoma_stomach_sacrococcigeal_heart



Phase1 CAGE Peaks

Hg19::chr15:63340604..63340622,+p7@TPM1
Hg19::chr15:63340647..63340728,+p2@TPM1
Hg19::chr15:63340734..63340769,+p4@TPM1


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism6.54e-29114
organ system subdivision7.04e-22223
anatomical cluster8.09e-22373
multi-tissue structure1.50e-16342
anatomical conduit1.43e-15240
multi-cellular organism1.96e-15656
neural tube3.82e-1356
neural rod3.82e-1356
future spinal cord3.82e-1356
neural keel3.82e-1356
anatomical system1.67e-12624
cell layer2.02e-12309
epithelium2.27e-12306
tube2.50e-12192
anatomical group3.45e-12625
central nervous system3.80e-1281
regional part of nervous system4.30e-1253
regional part of brain4.30e-1253
brain6.36e-1268
future brain6.36e-1268
nervous system1.42e-1189
regional part of forebrain1.29e-1041
forebrain1.29e-1041
anterior neural tube1.29e-1041
future forebrain1.29e-1041
embryo4.62e-10592
brain grey matter7.60e-1034
gray matter7.60e-1034
neural plate1.08e-0982
presumptive neural plate1.08e-0982
subdivision of digestive tract1.39e-09118
cerebral hemisphere1.66e-0932
telencephalon2.71e-0934
regional part of telencephalon3.52e-0932
regional part of cerebral cortex3.87e-0922
germ layer1.43e-08560
germ layer / neural crest1.43e-08560
embryonic tissue1.43e-08560
presumptive structure1.43e-08560
germ layer / neural crest derived structure1.43e-08560
epiblast (generic)1.43e-08560
embryonic structure1.72e-08564
digestive system2.36e-08145
digestive tract2.36e-08145
primitive gut2.36e-08145
developing anatomical structure2.41e-08581
neocortex3.14e-0820
organ3.50e-08503
structure with developmental contribution from neural crest4.96e-08132
cerebral cortex6.45e-0825
pallium6.45e-0825
ecto-epithelium7.25e-08104
neurectoderm7.91e-0886
organ part1.35e-07218
endoderm-derived structure3.41e-07160
endoderm3.41e-07160
presumptive endoderm3.41e-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)
MA0003.12.61626
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.12.91906
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.707589
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BCL3#602334.54710280373832.42397750207122e-050.000526753612856463
BCLAF1#9774321.65264761012189.8473954032885e-050.00139092795310258
CCNT2#90536.336201576962630.003930750035764890.0189679620655754
CTBP2#1488362.71700033932814.049570681927e-060.000129416497077654
CTCF#1066435.360256373075030.0064925092527670.027900718999701
CTCFL#140690319.74647435897440.0001298372005551160.00171472779321899
E2F1#186934.907389214879320.008460985347239390.0324563596811994
EGR1#195834.988179094810140.008056488137383440.0319879700646361
ELF1#199734.258097958807540.01295179875054610.0461238077439998
ELK4#2005316.2356816584680.0002336043955745990.00255470256224246
EP300#203336.77394172622320.003216880500103790.0167231350199273
ETS1#211339.728760922202340.001085840092584840.00760998882227001
GABPB1#255337.067683836182170.002832212825417420.0153866768244783
GATA1#2623313.56030814380040.0004009615963782630.00387453998558007
GTF2B#2959331.94382993432423.06634405746243e-050.000627072463319599
GTF2F1#2962312.73966087675770.0004835525047438590.00433342543701252
HDAC2#3066313.41562023662630.0004140761399857210.00390656711688967
HMGN3#932438.178547723350590.001827766942164210.0108540485399834
JUND#372736.994663941871030.002921845042734990.0156481500650325
NR3C1#2908314.9730233311730.0002978331194675480.0030840167721665
NRF1#4899312.21027944771090.0005492172401020010.00470431389641704
PAX5#507936.669565531177830.003370290999677260.017265405489542
RAD21#5885310.35503389545630.0009004912073565420.0066309244310167
REST#597839.650028716128020.001112636247114590.00766406918694108
RXRA#6256213.38307809275550.007196434429465730.0298225702475586
SMARCB1#6598318.25271578115740.000164397760679890.00202781832144172
SMC3#9126315.04493284493280.0002935825420371870.00308558590196455
STAT1#6772320.70658749719920.0001125992441046670.00154652189045861
TCF7L2#6934310.77017656313730.0008003181298398380.00612699202186944
TFAP2A#7020316.5186343730450.0002218033880766340.00247806205042101
TFAP2C#7022310.80922860986020.0007916746575753130.00614322829054968
THAP1#55145331.36914460285133.23800758564397e-050.000645863778145666
TRIM28#10155318.59052504526250.0001555969297255280.00196759749892292
USF1#739136.361499277207960.00388404057290560.0189962214757745
USF2#7392312.99219738506960.0004558979393427810.0042113501580595
YY1#752834.911170749853860.008441455341808260.0328667295870531
ZBTB7A#5134137.35190930787590.002516255860282270.0139881431730462
ZEB1#6935316.88843201754390.0002075486917327580.00242408608989907
ZNF143#7702313.50087655222790.0004062804962997170.00388424832964538



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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