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Coexpression cluster:C3441: Difference between revisions

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{{Coexpression_clusters
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516,0.20753,0.000373385,0.179412,0.193601,0.220904,0.0269454,0.341681,0.00651011,0.21801,0.198614,0.0186488,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.0172483,0.226869,0.27872,0.0855609,0.131118,0.0233967,0.0335483,0.222339,0.0673329,0.20847,0.266544,0.0066506,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.000311698,0.201602,0.350452,0.0126763,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.0367308,0.00371613,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.0219648,0.310405,0.280943,0.218161,0.0822373,0.0219487,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.0577193,0.0377035,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.00499908,0.347036,0.141729,0.0381402,0.0359756,8.667e-05,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.0213159,0.28689,0.236464,0.325148,0.115817,0.0257187,0.223831,0.11528,0.194982,0.190993,0.281727,0.00480369,1.2918e-05,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.056548,0.171683,0.0133429,0.271275,0.071111,0.0404514,0.101021,0.222548,0.175934,0.157274,0.215705,0.035048,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=1.66899,0.14394,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,0.491742,1.18351,0.820209,0.985163,0.436625,0.925331,1.54465,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,1.82956,0.259059,0.63803,2.07812,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,7.6454,1.45054,1.92922,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,2.62406,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,2.61709,0.921547,1.7605,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,2.36218,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,2.76728,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,2.60433,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,3.38286,1.08214,2.31409,1.82176,0.539692,1.54007,17.651,1.37083,0.481626,0.941179,1.78371,1.03563,1.51317,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.96295|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;1.93041,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.80735,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;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;1.70328,MA0059.1;0.714521,MA0060.1;2.13518,MA0061.1;1.15625,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;0.990225,MA0074.1;0.935474,MA0076.1;0.734647,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;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;1.55117,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;1.52002,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,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;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;2.11725,MA0146.1;1.16674,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.757898,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;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;2.02721,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;2.37721,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;1.84145,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;5.72079,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3441_Eosinophils_Mast_Neutrophils_Preadipocyte_CD14_Fibroblast_Smooth
|id=C3441
}}

Latest revision as of 12:26, 17 September 2013


Full id: C3441_Eosinophils_Mast_Neutrophils_Preadipocyte_CD14_Fibroblast_Smooth



Phase1 CAGE Peaks

Hg19::chr14:62162224..62162254,+p1@HIF1A
Hg19::chr14:62162258..62162269,+p2@HIF1A
Hg19::chr14:62162285..62162296,+p3@HIF1A


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>

Cell Type
Ontology termp-valuen
animal cell4.32e-26679
eukaryotic cell4.32e-26679
somatic cell2.57e-22588
multi fate stem cell7.98e-20427
somatic stem cell1.53e-18433
stem cell5.64e-18441
classical monocyte1.22e-1742
CD14-positive, CD16-negative classical monocyte1.22e-1742
defensive cell3.85e-1748
phagocyte3.85e-1748
native cell1.57e-16722
myeloid leukocyte5.71e-1572
muscle precursor cell6.15e-1358
myoblast6.15e-1358
multi-potent skeletal muscle stem cell6.15e-1358
monopoietic cell2.60e-1259
monocyte2.60e-1259
monoblast2.60e-1259
promonocyte2.60e-1259
macrophage dendritic cell progenitor6.57e-1261
fibroblast1.03e-1176
muscle cell1.70e-1155
granulocyte monocyte progenitor cell2.45e-1167
stuff accumulating cell4.32e-1187
myeloid lineage restricted progenitor cell2.85e-1066
contractile cell4.90e-1059
connective tissue cell9.17e-10361
mesenchymal cell2.88e-09354
electrically responsive cell5.73e-0961
electrically active cell5.73e-0961
smooth muscle cell4.88e-0843
smooth muscle myoblast4.88e-0843
vascular associated smooth muscle cell3.75e-0732
Uber Anatomy
Ontology termp-valuen
musculoskeletal system7.33e-22167
mesoderm4.75e-19315
mesoderm-derived structure4.75e-19315
presumptive mesoderm4.75e-19315
lateral plate mesoderm1.77e-12203
anatomical system4.51e-12624
skeletal element5.04e-1290
anatomical group7.26e-12625
multi-cellular organism7.36e-12656
skeletal system7.85e-12100
bone marrow1.29e-1176
bone element1.94e-1082
somite2.25e-1071
presomitic mesoderm2.25e-1071
presumptive segmental plate2.25e-1071
dermomyotome2.25e-1071
trunk paraxial mesoderm2.25e-1071
multilaminar epithelium2.59e-1083
skeletal muscle tissue4.21e-1062
striated muscle tissue4.21e-1062
myotome4.21e-1062
connective tissue4.71e-10371
paraxial mesoderm8.22e-1072
presumptive paraxial mesoderm8.22e-1072
dense mesenchyme tissue9.59e-1073
immune system2.80e-0993
muscle tissue4.54e-0964
musculature4.54e-0964
musculature of body4.54e-0964
epithelial vesicle8.28e-0978
embryonic structure9.90e-09564
germ layer1.80e-08560
germ layer / neural crest1.80e-08560
embryonic tissue1.80e-08560
presumptive structure1.80e-08560
germ layer / neural crest derived structure1.80e-08560
epiblast (generic)1.80e-08560
hematopoietic system2.92e-0898
blood island2.92e-0898
hemolymphoid system3.48e-08108
trunk mesenchyme3.69e-08122
developing anatomical structure5.27e-08581
embryo4.26e-07592


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
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.11.70328
MA0059.10.714521
MA0060.12.13518
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.990225
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.11725
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.12.37721
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.25.72079
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
ATF3#467322.46317452600878.81932387510763e-050.00129474468118128
BHLHE40#8553344.87181354697741.10603738662898e-050.00028423582338126
CCNT2#90536.336201576962630.003930750035764890.0189635810691634
CTCF#1066435.360256373075030.0064925092527670.0278880963169258
E2F1#186934.907389214879320.008460985347239390.0324384878925272
E2F6#187635.017155731697390.00791769806886330.032128233297615
EGR1#195834.988179094810140.008056488137383440.0319782443212294
ELF1#199734.258097958807540.01295179875054610.0461080856838901
ETS1#211339.728760922202340.001085840092584840.0076089676214082
FOS#235338.99795530889440.001372499272417130.00896170375192076
FOSL2#2355316.93020060456170.0002060162053171620.00242599238551348
GATA3#2625327.2365163572064.94721007899563e-050.000850085017177072
GTF2B#2959331.94382993432423.06634405746243e-050.000626826985745389
GTF2F1#2962312.73966087675770.0004835525047438590.00433193858663098
HDAC2#3066313.41562023662630.0004140761399857210.00390621425200693
HMGN3#932438.178547723350590.001827766942164210.0108528143540104
IRF1#365937.63716375356390.002244692747297240.0127826317249169
MAX#414936.452555509007120.003721913834265510.0186138466186302
MXI1#460139.96157162875930.001011470541259020.00719157000875151
MYC#460935.22228187160940.007020843755740150.0293864179627183
NFKB1#479035.488063424193840.006049381815655430.0269099321682101
NFYA#4800318.42558069983050.0001598135507814160.00199221382550255
NFYB#4801316.75979325353650.0002123649923296180.00245290725878268
PAX5#507936.669565531177830.003370290999677260.0172611721123624
PBX3#5090321.91451268674419.49854535978121e-050.00136378688318695
POU2F2#545239.106124057742520.001324165192682130.00880968840352459
REST#597839.650028716128020.001112636247114590.00766305836272755
SIN3A#2594235.408884726815140.006318961977991520.0275954869337009
SMARCB1#6598318.25271578115740.000164397760679890.00202757885305232
SMARCC1#6599343.66335931963151.20046018043203e-050.000301237051379483
SP1#666735.69838137814090.005403962701712170.0245972743780395
SREBF1#6720347.00584944048839.62099323994382e-060.000254317112879396
TAF7#6879311.43306940492390.0006690181981945830.00541724233224097
TCF12#6938310.63446490218640.0008313523990202070.00628669996388903
TCF7L2#6934310.77017656313730.0008003181298398380.00612609389932152
USF1#739136.361499277207960.00388404057290560.0189899964137301
USF2#7392312.99219738506960.0004558979393427810.00421023299027507
ZEB1#6935316.88843201754390.0002075486917327580.00242354403129221



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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