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Coexpression cluster:C391: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.989664594861199,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C391_large_bronchioalveolar_fibrosarcoma_lung_pancreatic_giant_testis|gostat_on_coexpression_clusters=GO:0007602!phototransduction!0.0060343812551513!2793$GO:0050908!detection of light stimulus during visual perception!0.0060343812551513!2793$GO:0050962!detection of light stimulus during sensory perception!0.0060343812551513!2793$GO:0009584!detection of visible light!0.0060343812551513!2793$GO:0009583!detection of light stimulus!0.0060343812551513!2793$GO:0005834!heterotrimeric G-protein complex!0.0060343812551513!2793$GO:0009582!detection of abiotic stimulus!0.0060343812551513!2793$GO:0050906!detection of stimulus during sensory perception!0.0060343812551513!2793$GO:0019897!extrinsic to plasma membrane!0.0060343812551513!2793$GO:0009581!detection of external stimulus!0.0060343812551513!2793$GO:0051606!detection of stimulus!0.00814641469445426!2793$GO:0009416!response to light stimulus!0.00814641469445426!2793$GO:0009314!response to radiation!0.00922398277573127!2793$GO:0019898!extrinsic to membrane!0.00922398277573127!2793$GO:0009628!response to abiotic stimulus!0.0132756387613329!2793$GO:0007601!visual perception!0.0158313767046911!2793$GO:0050953!sensory 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0.016908,0.410051,0.617826,0.489411,0.828033,0.577319,0.936947,0.719617,0.793248,0.874914,0.86463,0.952312,0.697639,0.471837,0.303832,0.890705,0.398776,0.667911,0.858013,0.851554,0.571895,0.80038,0.924874,0.801906,0.898267,0.586976,0.692338,0.669785,0.619452,0.596305,0.554522,0.0599949,0.816444,0.461014,0.54194,0.485157,0.77562,0.616519,0.661135,0.253782,0.785623,0.642183,0.927397,0.614052,0.378348|tfbs_overrepresentation_for_novel_motifs=0.0627807,0.0287104,0.472299,1.90655,0.683377,0.405344,0.175095,0.1716,0.333785,0.0158681,0.112658,0.58836,0.00725709,0.167821,0.679085,0.75352,0.33472,0.824868,0.0449306,0.0648405,0.216484,0.306,0.124907,0.667388,0.0793696,0.625087,0.0861865,0.391047,0.172973,0.157743,0.101256,0.363981,0.221705,0.112795,0.0333798,0.0470718,0.0324544,0.129917,2.05425,0.0105076,0.5728,0.310187,0.0733551,0.166623,0.65926,0.253512,0.175791,0.106932,1.10128,0.0454402,0.228909,0.183375,0.317077,0.427029,0.558863,0.169665,1.53983,0.149516,0.157534,0.148912,0.397292,0.177305,0.168594,0.313136,0.188939,3.95766,0.638114,0.983449,0.355656,0.828977,0.0867459,0.0689625,0.0368677,0.557091,0.0361178,0.00547592,0.310352,0.300172,0.353062,0.949615,0.46792,0.312308,1.05372,0.175848,0.511911,1.69998e-05,0.00647976,0.671849,0.24739,1.07932,0.723727,0.488513,0.984493,0.444129,0.0445871,0.256658,0.445998,0.412519,0.250711,0.0516711,0.502448,0.974418,0.407897,0.337605,0.762448,0.110252,0.325192,0.165662,0.0792544,0.039073,0.496755,1.04591,0.0576237,0.117734,0.679489,0.562692,0.00710701,0.330496,0.285144,0.732889,0.549768,0.245647,0.401357,0.57069,0.782053,0.300752,0.9826,0.381614,1.43518,0.48404,0.489108,0.336034,0.600533,0.193939,0.735665,0.423255,0.0982282,0.783203,0.696441,1.52541,1.13019,0.662221,1.56842,1.0546,0.279588,0.871902,0.737169,1.36826,0.305771,0.0913429,0.0763856,0.000259436,0.489437,0.156293,1.00669,0.857896,0.664556,0.155139,0.272485,0.236668,0.661111,0.47352,0.929056,1.33209,0.291674,1.65994,0.0818622,1.58048,5.09057e-06|tfbs_overrepresentation_jaspar=MA0003.1;5.02566e-06,MA0004.1;0.115462,MA0006.1;0.167736,MA0007.1;0.105458,MA0009.1;0.45361,MA0014.1;0.00010589,MA0017.1;0.463835,MA0019.1;0.596513,MA0024.1;0.366071,MA0025.1;0.570597,MA0027.1;2.00534,MA0028.1;0.185296,MA0029.1;0.993942,MA0030.1;0.372472,MA0031.1;0.320773,MA0038.1;1.00622,MA0040.1;0.38667,MA0041.1;0.396379,MA0042.1;0.108251,MA0043.1;0.453881,MA0046.1;0.444311,MA0048.1;0.0409853,MA0050.1;0.351951,MA0051.1;0.517477,MA0052.1;0.389861,MA0055.1;0.00211342,MA0056.1;0,MA0057.1;0.0910637,MA0058.1;0.0687016,MA0059.1;0.0681464,MA0060.1;5.37493,MA0061.1;0.129432,MA0063.1;0,MA0066.1;1.59719,MA0067.1;0.739032,MA0068.1;0.0831041,MA0069.1;0.441028,MA0070.1;0.431528,MA0071.1;0.464021,MA0072.1;0.427724,MA0073.1;1.73097e-13,MA0074.1;0.173668,MA0076.1;0.262185,MA0077.1;0.421218,MA0078.1;0.242013,MA0081.1;0.517137,MA0083.1;0.460049,MA0084.1;0.916043,MA0087.1;0.425657,MA0088.1;0.360903,MA0089.1;0,MA0090.1;2.03295,MA0091.1;0.751442,MA0092.1;0.0969694,MA0093.1;0.0447606,MA0095.1;0,MA0098.1;0,MA0100.1;0.546121,MA0101.1;0.393842,MA0103.1;0.361926,MA0105.1;0.0736484,MA0106.1;0.204305,MA0107.1;0.472748,MA0108.2;0.318371,MA0109.1;0,MA0111.1;0.298621,MA0113.1;0.2156,MA0114.1;0.458087,MA0115.1;0.668285,MA0116.1;0.105451,MA0117.1;0.486035,MA0119.1;0.221145,MA0122.1;1.26786,MA0124.1;0.630319,MA0125.1;1.36549,MA0130.1;0,MA0131.1;0.255226,MA0132.1;0,MA0133.1;0,MA0135.1;1.20615,MA0136.1;0.535282,MA0139.1;0.0397016,MA0140.1;0.459966,MA0141.1;0.0674008,MA0142.1;0.296096,MA0143.1;0.215723,MA0144.1;0.217815,MA0145.1;0.0147495,MA0146.1;0.000996002,MA0147.1;0.0256229,MA0148.1;0.129389,MA0149.1;0.145006,MA0062.2;0.122342,MA0035.2;0.458892,MA0039.2;0.00286767,MA0138.2;0.242899,MA0002.2;0.304877,MA0137.2;0.192569,MA0104.2;0.0630844,MA0047.2;0.196083,MA0112.2;0.00301513,MA0065.2;0.0952518,MA0150.1;0.0796342,MA0151.1;0,MA0152.1;0.154883,MA0153.1;0.539635,MA0154.1;0.0704599,MA0155.1;0.0105966,MA0156.1;0.432724,MA0157.1;0.275302,MA0158.1;0,MA0159.1;0.265053,MA0160.1;0.138224,MA0161.1;0,MA0162.1;7.7782e-05,MA0163.1;0.000608073,MA0164.1;0.224291,MA0080.2;0.171095,MA0018.2;0.205249,MA0099.2;1.46826,MA0079.2;6.68155e-09,MA0102.2;0.951693,MA0258.1;0.391387,MA0259.1;0.0278251,MA0442.1;0}}
|full_id=C391_large_bronchioalveolar_fibrosarcoma_lung_pancreatic_giant_testis
|id=C391
}}

Latest revision as of 11:21, 17 September 2013


Full id: C391_large_bronchioalveolar_fibrosarcoma_lung_pancreatic_giant_testis



Phase1 CAGE Peaks

Hg19::chr10:4822880..4822903,-p@chr10:4822880..4822903
-
Hg19::chr10:4822908..4822927,-p@chr10:4822908..4822927
-
Hg19::chr10:4822941..4822949,-p@chr10:4822941..4822949
-
Hg19::chr11:75719740..75719766,+p@chr11:75719740..75719766
+
Hg19::chr12:122430653..122430662,+p@chr12:122430653..122430662
+
Hg19::chr12:21815245..21815251,+p1@ENST00000541860
Hg19::chr12:75174802..75174809,+p@chr12:75174802..75174809
+
Hg19::chr13:109644678..109644725,+p@chr13:109644678..109644725
+
Hg19::chr17:47286603..47286624,-p4@GNGT2
Hg19::chr1:33886864..33886872,-p@chr1:33886864..33886872
-
Hg19::chr1:33886874..33886882,-p@chr1:33886874..33886882
-
Hg19::chr1:8251750..8251759,+p@chr1:8251750..8251759
+
Hg19::chr2:33589897..33589917,+p@chr2:33589897..33589917
+
Hg19::chr2:45797888..45797917,-p@chr2:45797888..45797917
-
Hg19::chr2:45797921..45797939,-p@chr2:45797921..45797939
-
Hg19::chr2:75145327..75145329,+p9@ENST00000435984
Hg19::chr3:25894063..25894094,+p@chr3:25894063..25894094
+
Hg19::chr3:26426173..26426176,+p@chr3:26426173..26426176
+
Hg19::chr4:189864076..189864089,+p@chr4:189864076..189864089
+
Hg19::chr5:142638718..142638753,+p@chr5:142638718..142638753
+
Hg19::chr5:92526866..92526914,-p@chr5:92526866..92526914
-
Hg19::chr6:56765635..56765674,-p@chr6:56765635..56765674
-
Hg19::chr6:56765738..56765745,-p@chr6:56765738..56765745
-
Hg19::chr6:707779..707821,+p@chr6:707779..707821
+
Hg19::chr7:100810718..100810739,-p@chr7:100810718..100810739
-
Hg19::chrX:105065622..105065627,+p@chrX:105065622..105065627
+
Hg19::chrX:45474991..45474996,+p@chrX:45474991..45474996
+


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

GO IDGO nameFDR corrected p-value
GO:0007602phototransduction0.0060343812551513
GO:0050908detection of light stimulus during visual perception0.0060343812551513
GO:0050962detection of light stimulus during sensory perception0.0060343812551513
GO:0009584detection of visible light0.0060343812551513
GO:0009583detection of light stimulus0.0060343812551513
GO:0005834heterotrimeric G-protein complex0.0060343812551513
GO:0009582detection of abiotic stimulus0.0060343812551513
GO:0050906detection of stimulus during sensory perception0.0060343812551513
GO:0019897extrinsic to plasma membrane0.0060343812551513
GO:0009581detection of external stimulus0.0060343812551513
GO:0051606detection of stimulus0.00814641469445426
GO:0009416response to light stimulus0.00814641469445426
GO:0009314response to radiation0.00922398277573127
GO:0019898extrinsic to membrane0.00922398277573127
GO:0009628response to abiotic stimulus0.0132756387613329
GO:0007601visual perception0.0158313767046911
GO:0050953sensory perception of light stimulus0.0158313767046911
GO:0003924GTPase activity0.0183713384879051
GO:0009605response to external stimulus0.0402080351001134



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 cell of lung6.95e-1219
Uber Anatomy
Ontology termp-valuen
respiratory tract epithelium6.95e-1219
lung epithelium6.95e-1219
lung1.80e-1022
respiratory tube1.80e-1022
respiration organ1.80e-1022
pair of lungs1.80e-1022
lung primordium1.80e-1022
lung bud1.80e-1022
respiratory system epithelium1.52e-0828
thoracic cavity element2.74e-0734
thoracic cavity2.74e-0734
thoracic segment organ4.03e-0735
epithelial bud8.21e-0737
Disease
Ontology termp-valuen
lung large cell carcinoma2.39e-663
non-small cell lung carcinoma1.48e-405
lung carcinoma2.62e-239
lung cancer1.22e-1415
respiratory system cancer8.02e-1416


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)
MA0003.15.02566e-06
MA0004.10.115462
MA0006.10.167736
MA0007.10.105458
MA0009.10.45361
MA0014.10.00010589
MA0017.10.463835
MA0019.10.596513
MA0024.10.366071
MA0025.10.570597
MA0027.12.00534
MA0028.10.185296
MA0029.10.993942
MA0030.10.372472
MA0031.10.320773
MA0038.11.00622
MA0040.10.38667
MA0041.10.396379
MA0042.10.108251
MA0043.10.453881
MA0046.10.444311
MA0048.10.0409853
MA0050.10.351951
MA0051.10.517477
MA0052.10.389861
MA0055.10.00211342
MA0056.10
MA0057.10.0910637
MA0058.10.0687016
MA0059.10.0681464
MA0060.15.37493
MA0061.10.129432
MA0063.10
MA0066.11.59719
MA0067.10.739032
MA0068.10.0831041
MA0069.10.441028
MA0070.10.431528
MA0071.10.464021
MA0072.10.427724
MA0073.11.73097e-13
MA0074.10.173668
MA0076.10.262185
MA0077.10.421218
MA0078.10.242013
MA0081.10.517137
MA0083.10.460049
MA0084.10.916043
MA0087.10.425657
MA0088.10.360903
MA0089.10
MA0090.12.03295
MA0091.10.751442
MA0092.10.0969694
MA0093.10.0447606
MA0095.10
MA0098.10
MA0100.10.546121
MA0101.10.393842
MA0103.10.361926
MA0105.10.0736484
MA0106.10.204305
MA0107.10.472748
MA0108.20.318371
MA0109.10
MA0111.10.298621
MA0113.10.2156
MA0114.10.458087
MA0115.10.668285
MA0116.10.105451
MA0117.10.486035
MA0119.10.221145
MA0122.11.26786
MA0124.10.630319
MA0125.11.36549
MA0130.10
MA0131.10.255226
MA0132.10
MA0133.10
MA0135.11.20615
MA0136.10.535282
MA0139.10.0397016
MA0140.10.459966
MA0141.10.0674008
MA0142.10.296096
MA0143.10.215723
MA0144.10.217815
MA0145.10.0147495
MA0146.10.000996002
MA0147.10.0256229
MA0148.10.129389
MA0149.10.145006
MA0062.20.122342
MA0035.20.458892
MA0039.20.00286767
MA0138.20.242899
MA0002.20.304877
MA0137.20.192569
MA0104.20.0630844
MA0047.20.196083
MA0112.20.00301513
MA0065.20.0952518
MA0150.10.0796342
MA0151.10
MA0152.10.154883
MA0153.10.539635
MA0154.10.0704599
MA0155.10.0105966
MA0156.10.432724
MA0157.10.275302
MA0158.10
MA0159.10.265053
MA0160.10.138224
MA0161.10
MA0162.17.7782e-05
MA0163.10.000608073
MA0164.10.224291
MA0080.20.171095
MA0018.20.205249
MA0099.21.46826
MA0079.26.68155e-09
MA0102.20.951693
MA0258.10.391387
MA0259.10.0278251
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
FOS#235382.666060832265010.007361706011402330.0304350096637181



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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