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Coexpression cluster:C4505: Difference between revisions

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{{Coexpression_clusters
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,0.258496,0.261744,0.203781,0.00193951,0.207559,0.141867,0.00140109,0.249101,0.115972,0.224568,0.246105,4.66494e-05,0.0215816,0.139785,0.197112,0.240478,0.00072309,0.13108,0.256963,0.222798,0.000975743,0.176789,0.0969345,9.05035e-05,0.00649151,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.000648679,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,9.53285e-05,0.0981146,0.064145,0.121913,0.00208455,0.000206969,0.0663259,0.0762523,0.000393514,0.109171,0.000987475,0.066952,0.089609,0.0367455,0.000455851,0.204393,0.295769,0.0457063,0.00940743,0.141729,0.0037817,0.0359756,0.200105,0.227491,0.29837,0.253509,0.177664,0.00482769,0.00384051,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.00135479,0.281727,0.283218,0.000226794,0.164638,0.224257,0.0935776,0.327622,0.225752,0.0232618,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.0268373,0.00104522,0.157274,0.215705,0.252796,0.205954,0.0750181|tfbs_overrepresentation_for_novel_motifs=2.80639,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,1.86765,1.21459,1.3235,0.439574,0.599922,0.137917,2.47502,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,2.33699,2.18821,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,1.5923,1.45054,0.430728,2.79908,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,2.62406,1.37703,0.450952,4.59048,1.05794,0.360456,2.38768,1.22626,4.57281,1.1798,1.09802,0.815119,1.16312,0.921547,2.94614,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.188952,0.794219,2.50498,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.99724,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,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;0.658629,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;2.45333,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;2.37507,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;5.46492,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;1.79391,MA0074.1;0.935474,MA0076.1;1.74184,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;1.70054,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.715722,MA0089.1;0,MA0090.1;0.751469,MA0091.1;1.93651,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;4.2163,MA0109.1;0,MA0111.1;0.767139,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;1.12079,MA0140.1;2.07172,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;2.94723,MA0146.1;0.707589,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;2.15877,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;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.311277,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4505_acute_pineal_skin_occipital_parietal_colon_brain
|id=C4505
}}

Latest revision as of 14:14, 17 September 2013


Full id: C4505_acute_pineal_skin_occipital_parietal_colon_brain



Phase1 CAGE Peaks

Hg19::chr5:53606354..53606372,-p3@ARL15
Hg19::chr5:53606375..53606394,-p2@ARL15
Hg19::chr5:53606396..53606431,-p1@ARL15


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.95e-33114
central nervous system2.54e-1381
neural tube3.78e-1256
neural rod3.78e-1256
future spinal cord3.78e-1256
neural keel3.78e-1256
regional part of forebrain9.50e-1241
forebrain9.50e-1241
anterior neural tube9.50e-1241
future forebrain9.50e-1241
nervous system2.88e-1189
hemolymphoid system4.47e-11108
hematopoietic system5.07e-1198
blood island5.07e-1198
regional part of nervous system7.51e-1153
regional part of brain7.51e-1153
brain2.90e-1068
future brain2.90e-1068
regional part of cerebral cortex1.00e-0922
brain grey matter1.73e-0934
gray matter1.73e-0934
telencephalon2.86e-0934
cerebral hemisphere3.20e-0932
regional part of telencephalon4.69e-0932
neocortex1.03e-0820
immune system1.05e-0893
cerebral cortex8.52e-0825
pallium8.52e-0825
bone element1.71e-0782
bone marrow2.30e-0776


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
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.12.37507
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.15.46492
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
MA0073.11.79391
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.11.93651
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
MA0108.24.2163
MA0109.10
MA0111.10.767139
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
MA0139.11.12079
MA0140.12.07172
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.94723
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
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
CCNT2#90536.336201576962630.003930750035764890.0190887939637891
CEBPB#105137.971147625824820.001974187055288560.0115637757637286
CHD2#1106310.34402283411690.0009033701102746880.00662410102836328
E2F1#186934.907389214879320.008460985347239390.0327183371104982
E2F6#187635.017155731697390.00791769806886330.0323925285417586
EGR1#195834.988179094810140.008056488137383440.032209607035187
ELF1#199734.258097958807540.01295179875054610.0464484894481245
EP300#203336.77394172622320.003216880500103790.0168160459757916
FOS#235338.99795530889440.001372499272417130.0090090158702767
FOXA1#3169311.08141974938550.000734755275698670.00583330340088889
GATA1#2623313.56030814380040.0004009615963782630.00389146251873891
GATA2#2624312.7449317335540.0004829527704283790.00438524642590589
GATA3#2625327.2365163572064.94721007899563e-050.000853596024186725
GTF2B#2959331.94382993432423.06634405746243e-050.000629414125427121
GTF2F1#2962312.73966087675770.0004835525047438590.00435547563975368
HMGN3#932438.178547723350590.001827766942164210.0109073853878457
HNF4G#3174328.75342252644684.20470658818262e-050.000759618320988073
JUND#372736.994663941871030.002921845042734990.0157442252821277
MAFF#23764356.31535648994525.59409009993116e-060.00016924715409812
MXI1#460139.96157162875930.001011470541259020.00722551107103632
NFKB1#479035.488063424193840.006049381815655430.0270620829026488
NFYA#4800318.42558069983050.0001598135507814160.00200153105049291
NFYB#4801316.75979325353650.0002123649923296180.00246544991484137
NR3C1#2908314.9730233311730.0002978331194675480.00309845534057887
PBX3#5090321.91451268674419.49854535978121e-050.0013726561212539
POU2F2#545239.106124057742520.001324165192682130.00885084726774585
RDBP#79363153.6384039900252.75057764221434e-071.4054186808964e-05
REST#597839.650028716128020.001112636247114590.00770472198729616
RFX5#5993312.04791082719510.0005717246050312580.00486240602808303
SIN3A#2594235.408884726815140.006318961977991520.0277953952752161
SMARCB1#6598318.25271578115740.000164397760679890.00203792732672368
SP1#666735.69838137814090.005403962701712170.0247634794701469
TAF7#6879311.43306940492390.0006690181981945830.00545062731892067
TAL1#6886329.86861667744023.75103522793067e-050.000721728754918664
TCF12#6938310.63446490218640.0008313523990202070.00631413084148581
TCF7L2#6934310.77017656313730.0008003181298398380.0061658619919108
YY1#752834.911170749853860.008441455341808260.0330900106760918



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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