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Coexpression cluster:C4071: Difference between revisions

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{{Coexpression_clusters
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11332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.00553696,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.0280973,0.0497481,0.253509,0.0168099,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.000125371,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.000158246,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=2.80639,0.14394,1.65103,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,1.54465,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,1.96998,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,1.96994,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,2.18821,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,2.0644,1.25741,0.941709,0.492369,1.14672,0.961293,2.51002,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,1.76229,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,2.35823,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,1.90788,1.16312,0.921547,0.743661,0.622396,1.67826,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,3.53119,2.76728,1.48578,1.37952,1.37044,0.798812,5.26928,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,2.04753,1.08214,2.31409,1.82176,0.539692,0.318511,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,1.69998,1.11698,0.960047,0.524529,0.936473,0.0768232|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;2.94911,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;3.88968,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;0.341392,MA0050.1;1.90116,MA0051.1;3.54769,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;2.4146,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;2.1667,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;0.211629,MA0074.1;2.15449,MA0076.1;2.91768,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;2.59836,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;2.32521,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;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.752137,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;4.02533,MA0035.2;0.894194,MA0039.2;0.0526989,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;2.13692,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;2.02335,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;1.55139,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.00160703,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4071_Mast_testicular_CD34_peripheral_skeletal_nonsmall_lung
|id=C4071
}}

Latest revision as of 12:38, 17 September 2013


Full id: C4071_Mast_testicular_CD34_peripheral_skeletal_nonsmall_lung



Phase1 CAGE Peaks

Hg19::chr21:27107323..27107334,-p5@ATP5J
Hg19::chr21:27107346..27107357,-p4@ATP5J
Hg19::chr21:27107359..27107370,-p3@ATP5J


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
central nervous system2.15e-1981
nervous system3.68e-1889
neurectoderm2.61e-1686
brain6.57e-1668
future brain6.57e-1668
neural plate6.12e-1582
presumptive neural plate6.12e-1582
neural tube7.25e-1556
neural rod7.25e-1556
future spinal cord7.25e-1556
neural keel7.25e-1556
regional part of nervous system1.17e-1453
regional part of brain1.17e-1453
adult organism1.53e-14114
regional part of forebrain1.79e-1441
forebrain1.79e-1441
anterior neural tube1.79e-1441
future forebrain1.79e-1441
cerebral hemisphere7.40e-1332
telencephalon8.96e-1334
pre-chordal neural plate2.20e-1261
regional part of telencephalon5.18e-1232
brain grey matter1.48e-1134
gray matter1.48e-1134
structure with developmental contribution from neural crest5.05e-11132
regional part of cerebral cortex9.64e-1122
ectoderm-derived structure1.03e-10171
ectoderm1.03e-10171
presumptive ectoderm1.03e-10171
cerebral cortex2.64e-1025
pallium2.64e-1025
neocortex6.47e-1020
ecto-epithelium2.10e-08104
anatomical cluster7.62e-07373


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.12.94911
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.13.88968
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
MA0048.10.341392
MA0050.11.90116
MA0051.13.54769
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.12.4146
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.12.15449
MA0076.12.91768
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
MA0108.22.59836
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.24.02533
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.22.13692
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.12.02335
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
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
BCLAF1#9774321.65264761012189.8473954032885e-050.001393189011818
CCNT2#90536.336201576962630.003930750035764890.0190339207615564
CHD2#1106310.34402283411690.0009033701102746880.0066115676907483
CTCF#1066435.360256373075030.0064925092527670.0279963325288907
E2F1#186934.907389214879320.008460985347239390.0325952360265708
E2F6#187635.017155731697390.00791769806886330.0322888117381497
EGR1#195834.988179094810140.008056488137383440.0321198490067258
ELF1#199734.258097958807540.01295179875054610.0463133122096855
ELK4#2005316.2356816584680.0002336043955745990.00255952680123957
EP300#203336.77394172622320.003216880500103790.0167715546400929
ETS1#211339.728760922202340.001085840092584840.00763406620191637
GABPB1#255337.067683836182170.002832212825417420.0154364615005621
GTF2F1#2962312.73966087675770.0004835525047438590.0043464790466429
HDAC2#3066313.41562023662630.0004140761399857210.00391824752957948
IRF1#365937.63716375356390.002244692747297240.0128302028149615
IRF4#3662321.91451268674419.49854535978121e-050.00136830148804164
JUND#372736.994663941871030.002921845042734990.0157020980970567
MAX#414936.452555509007120.003721913834265510.0186863262636696
MEF2C#4208341.31135449262411.41744912101957e-050.000340549732574564
MYC#460935.22228187160940.007020843755740150.0294987287687873
NFKB1#479035.488063424193840.006049381815655430.0269973244784735
NR2C2#7182332.61461090524092.88098172333076e-050.000605406137229259
NRF1#4899312.21027944771090.0005492172401020010.00471708053774777
PAX5#507936.669565531177830.003370290999677260.0173155166133065
POU2F2#545239.106124057742520.001324165192682130.00883219367470488
RFX5#5993312.04791082719510.0005717246050312580.00485371045560556
RXRA#6256320.07461713913330.0001235730348432220.00165395927027955
SETDB1#9869340.32002617801051.52461559299059e-050.000359353030729732
SIN3A#2594235.408884726815140.006318961977991520.027725331681698
SIX5#147912317.0867153554590.0002004060546325010.00239942771291571
SP1#666735.69838137814090.005403962701712170.0246941352266076
SPI1#668838.204323508522730.001810593189410520.0109197056134922
SRF#6722313.79717826216780.0003806615025800190.0037558721462404
TRIM28#10155318.59052504526250.0001555969297255280.00197357150153077
USF1#739136.361499277207960.00388404057290560.019062279764741
USF2#7392312.99219738506960.0004558979393427810.00422143141120851
WRNIP1#568973109.8199643493767.53682839543883e-073.32828254034349e-05
YY1#752834.911170749853860.008441455341808260.032990949909932
ZEB1#6935316.88843201754390.0002075486917327580.00243060975733096
ZNF143#7702313.50087655222790.0004062804962997170.00389709117864127



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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