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Coexpression cluster:C3260: Difference between revisions

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{{Coexpression_clusters
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26,0.200432,0.0102599,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.00467879,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,1.23863,0.491742,2.59717,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,1.49369,0.69094,1.26332,1.96998,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,6.17058,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,2.20718,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,1.10051,0.414196,1.02656,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.22068,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,1.94007,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,3.36921,0.318511,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;4.57391,MA0004.1;0.826076,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;5.19826,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;0.886807,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;1.79391,MA0074.1;0.935474,MA0076.1;5.6086,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;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;1.55947,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;3.85295,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;8.94965,MA0035.2;0.894194,MA0039.2;1.15986,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;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;2.05956,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;2.70224,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3260_Alveolar_Renal_hepatoblastoma_Keratinocyte_Bronchial_Endothelial_granulocyte
|id=C3260
}}

Latest revision as of 12:22, 17 September 2013


Full id: C3260_Alveolar_Renal_hepatoblastoma_Keratinocyte_Bronchial_Endothelial_granulocyte



Phase1 CAGE Peaks

Hg19::chr12:133287378..133287390,+p3@PGAM5
Hg19::chr12:133287392..133287412,+p2@PGAM5
Hg19::chr12:133287419..133287465,+p1@PGAM5


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell9.85e-34253
embryonic cell4.76e-20250
animal cell8.69e-15679
eukaryotic cell8.69e-15679
endodermal cell1.40e-0958
squamous epithelial cell2.14e-0963
epithelial cell of nephron4.57e-0815
endo-epithelial cell2.71e-0742
kidney cortical cell2.93e-0712
renal cortical epithelial cell2.93e-0712
native cell5.13e-07722
kidney cell5.77e-0717
kidney epithelial cell5.77e-0717
mesodermal cell6.39e-07121
Uber Anatomy
Ontology termp-valuen
trunk region element1.08e-13101
organism subdivision6.15e-12264
trunk1.22e-11199
segment of respiratory tract3.67e-0947
subdivision of trunk5.82e-09112
unilaminar epithelium8.99e-09148
endoderm-derived structure1.33e-08160
endoderm1.33e-08160
presumptive endoderm1.33e-08160
foregut1.81e-0887
nephron epithelium4.57e-0815
renal tubule4.57e-0815
nephron tubule4.57e-0815
nephron4.57e-0815
uriniferous tubule4.57e-0815
nephrogenic mesenchyme4.57e-0815
cortex4.91e-0815
respiratory primordium6.29e-0838
endoderm of foregut6.29e-0838
digestive system1.30e-07145
digestive tract1.30e-07145
primitive gut1.30e-07145
subdivision of digestive tract1.33e-07118
abdomen element1.46e-0754
abdominal segment element1.46e-0754
urinary system structure2.21e-0747
excretory tube2.49e-0716
kidney epithelium2.49e-0716
cortex of kidney2.93e-0712
renal parenchyma2.93e-0712
respiratory tract3.08e-0754
renal system3.52e-0748
kidney4.02e-0726
kidney mesenchyme4.02e-0726
upper urinary tract4.02e-0726
kidney rudiment4.02e-0726
kidney field4.02e-0726
epithelial tube4.14e-07117
mesenchyme7.20e-07160
entire embryonic mesenchyme7.20e-07160
respiratory system9.37e-0774
Disease
Ontology termp-valuen
cancer5.14e-30235
disease of cellular proliferation3.22e-29239
carcinoma2.21e-17106
cell type cancer6.43e-17143
organ system cancer1.08e-15137
hematologic cancer4.30e-1251
immune system cancer4.30e-1251
leukemia3.41e-0939
myeloid leukemia1.73e-0731


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)
MA0003.14.57391
MA0004.10.826076
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
MA0028.15.19826
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
MA0057.10.886807
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
MA0073.11.79391
MA0074.10.935474
MA0076.15.6086
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
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
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
MA0145.13.85295
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.28.94965
MA0035.20.894194
MA0039.21.15986
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
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.70224
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-050.00138923696950432
BRCA1#672320.18423064322380.0001215704860271640.00163976494771935
CCNT2#90536.336201576962630.003930750035764890.0189382111447732
CHD2#1106310.34402283411690.0009033701102746880.0065889427297282
E2F1#186934.907389214879320.008460985347239390.0323980512806722
E2F4#1874312.66806031528440.0004917987006298980.00435981364019064
E2F6#187635.017155731697390.00791769806886330.0320821132342973
EGR1#195834.988179094810140.008056488137383440.0319406128603496
ELF1#199734.258097958807540.01295179875054610.0460484394794309
ELK4#2005316.2356816584680.0002336043955745990.0025514964933503
ETS1#211339.728760922202340.001085840092584840.00760539557571375
GABPB1#255337.067683836182170.002832212825417420.0153706856824865
HDAC2#3066313.41562023662630.0004140761399857210.00390092891791166
HMGN3#932438.178547723350590.001827766942164210.0108423350944387
HSF1#32973164.2906666666672.24910326529255e-071.18993969566306e-05
MAX#414936.452555509007120.003721913834265510.0185942577821983
MXI1#460139.96157162875930.001011470541259020.00718716640757593
MYC#460935.22228187160940.007020843755740150.0293440811992055
NFKB1#479035.488063424193840.006049381815655430.0268790209506589
NR3C1#2908314.9730233311730.0002978331194675480.00308157253458206
NRF1#4899312.21027944771090.0005492172401020010.00469891859908355
PAX5#507936.669565531177830.003370290999677260.0172451041945663
POU2F2#545239.106124057742520.001324165192682130.0088018386302526
PPARGC1A#108913350.0511363636362.31814761783079e-081.63474016920074e-06
SIN3A#2594235.408884726815140.006318961977991520.027571276321
SIX5#147912317.0867153554590.0002004060546325010.00239147714119787
SP1#666735.69838137814090.005403962701712170.0245672946765384
SP2#6668326.15353049384465.58768218891694e-050.00093836941651117
SPI1#668838.204323508522730.001810593189410520.0108863869953279
TCF12#6938310.63446490218640.0008313523990202070.00628078799199012
USF2#7392312.99219738506960.0004558979393427810.00420688504037999
YY1#752834.911170749853860.008441455341808260.0328239009063298
ZBTB33#10009331.66472502998123.14815888737575e-050.000633263802077496
ZEB1#6935316.88843201754390.0002075486917327580.00242218994478461



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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