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Coexpression cluster:C3624: Difference between revisions

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|full_id=C3624_cerebellum_serous_papillary_Renal_signet_teratocarcinoma_osteosarcoma
|full_id=C3624_cerebellum_serous_papillary_Renal_signet_teratocarcinoma_osteosarcoma
|id=C3624
|id=C3624
|ontology_enrichment_celltype=CL:0000066!1.54e-12!254;CL:1000497!3.66e-12!18;CL:0002518!3.66e-12!18;CL:1000507!1.35e-11!12;CL:1000494!1.35e-11!12;CL:1000449!6.12e-11!16;CL:0002681!7.87e-08!13;CL:0002584!7.87e-08!13;CL:0000077!2.73e-07!19;CL:0002319!5.26e-07!25
|ontology_enrichment_celltype=CL:1000507!4.40e-18!10;CL:1000494!4.40e-18!10;CL:1000449!1.08e-15!15;CL:1000497!1.99e-13!17;CL:0002518!1.99e-13!17;CL:0002681!5.28e-11!12;CL:0002584!5.28e-11!12;CL:0000066!1.32e-09!253
|ontology_enrichment_disease=DOID:305!9.61e-13!106;DOID:0050687!7.19e-12!143;DOID:162!6.91e-11!235;DOID:14566!3.59e-10!239
|ontology_enrichment_disease=DOID:305!6.76e-10!106;DOID:0050687!1.17e-09!143;DOID:162!7.93e-09!235;DOID:14566!2.40e-08!239
|ontology_enrichment_uberon=UBERON:0000489!3.49e-22!32;UBERON:0002113!1.61e-18!27;UBERON:0003918!1.61e-18!27;UBERON:0005095!1.61e-18!27;UBERON:0007687!1.61e-18!27;UBERON:0005743!1.50e-14!86;UBERON:0001017!1.85e-13!82;UBERON:0000073!4.31e-13!94;UBERON:0001016!4.31e-13!94;UBERON:0003886!7.79e-13!63;UBERON:0003103!7.99e-13!69;UBERON:0006554!8.54e-13!44;UBERON:0000080!9.05e-13!18;UBERON:0002120!9.05e-13!18;UBERON:0004875!9.05e-13!18;UBERON:0005721!9.05e-13!18;UBERON:0005754!9.05e-13!18;UBERON:0007297!9.05e-13!18;UBERON:0003076!1.45e-12!15;UBERON:0003057!1.45e-12!15;UBERON:0001008!2.69e-12!45;UBERON:0006555!8.57e-12!17;UBERON:0005103!8.57e-12!17;UBERON:0000083!8.57e-12!17;UBERON:0009201!8.57e-12!17;UBERON:0004819!8.57e-12!17;UBERON:0006553!8.57e-12!17;UBERON:0003074!8.57e-12!17;UBERON:0003060!8.57e-12!17;UBERON:0005177!1.11e-11!107;UBERON:0009773!1.35e-11!12;UBERON:0001231!1.35e-11!12;UBERON:0004810!1.35e-11!12;UBERON:0002553!2.35e-11!70;UBERON:0003887!3.03e-11!21;UBERON:0004876!6.03e-11!20;UBERON:0004211!6.12e-11!16;UBERON:0001285!6.12e-11!16;UBERON:0007684!6.12e-11!16;UBERON:0003220!6.12e-11!16;UBERON:0004208!6.12e-11!16;UBERON:0004733!4.00e-10!12;UBERON:0002028!4.00e-10!12;UBERON:0007277!4.00e-10!12;UBERON:0000464!5.63e-10!104;UBERON:0000058!1.18e-09!26;UBERON:0000955!1.81e-09!69;UBERON:0006238!1.81e-09!69;UBERON:0000033!3.33e-09!123;UBERON:0004732!4.48e-09!13;UBERON:0004121!5.23e-09!169;UBERON:0000924!8.58e-09!173;UBERON:0006601!8.58e-09!173;UBERON:0005172!1.17e-08!55;UBERON:0005173!1.17e-08!55;UBERON:0000475!2.34e-08!365;UBERON:0003075!2.50e-08!86;UBERON:0007284!2.50e-08!86;UBERON:0001049!2.97e-08!57;UBERON:0005068!2.97e-08!57;UBERON:0006241!2.97e-08!57;UBERON:0007135!2.97e-08!57;UBERON:0003064!3.99e-08!37;UBERON:0000153!4.02e-08!129;UBERON:0007811!4.02e-08!129;UBERON:0002346!5.88e-08!90;UBERON:0001225!7.87e-08!13;UBERON:0008987!7.87e-08!13;UBERON:0002680!1.83e-07!9;UBERON:0001895!1.83e-07!9;UBERON:0010092!1.83e-07!9;UBERON:0001851!4.53e-07!16;UBERON:0000466!5.17e-07!126;UBERON:0002417!5.54e-07!61;UBERON:0000916!5.54e-07!61
|ontology_enrichment_uberon=UBERON:0000489!4.72e-24!31;UBERON:0002113!1.48e-22!26;UBERON:0003918!1.48e-22!26;UBERON:0011143!1.48e-22!26;UBERON:0005095!1.48e-22!26;UBERON:0007687!1.48e-22!26;UBERON:0004810!4.40e-18!10;UBERON:0006555!6.94e-17!16;UBERON:0004819!6.94e-17!16;UBERON:0004211!1.08e-15!15;UBERON:0009773!1.08e-15!15;UBERON:0001231!1.08e-15!15;UBERON:0001285!1.08e-15!15;UBERON:0007684!1.08e-15!15;UBERON:0004208!1.08e-15!15;UBERON:0003076!2.23e-14!15;UBERON:0003057!2.23e-14!15;UBERON:0004733!3.70e-13!12;UBERON:0002028!3.70e-13!12;UBERON:0007277!3.70e-13!12;UBERON:0005177!2.31e-12!101;UBERON:0006554!3.63e-12!47;UBERON:0004732!6.06e-12!13;UBERON:0003103!7.19e-12!68;UBERON:0001008!8.88e-12!48;UBERON:0001225!5.28e-11!12;UBERON:0008987!5.28e-11!12;UBERON:0005172!6.99e-11!54;UBERON:0005173!6.99e-11!54;UBERON:0001851!2.50e-10!15;UBERON:0002298!3.10e-10!6;UBERON:0002680!3.28e-09!9;UBERON:0001895!3.28e-09!9;UBERON:0010092!3.28e-09!9;UBERON:0002417!3.80e-09!60;UBERON:0000916!3.80e-09!60;UBERON:0000353!2.34e-08!15;UBERON:0001017!1.86e-07!81;UBERON:0000062!3.10e-07!503;UBERON:0000955!9.03e-07!68;UBERON:0006238!9.03e-07!68
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321669766450389!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245535120490568
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321669766450389!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245535120490568
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1,0.406014,0.000384304,0.175785,0.184486,0.015204,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.0419304,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.00796449,0.0906475,3.02301e-05,2.5572e-05,0.0377931,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.0199999,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.00340073,0.170307,0.201033,2.02233e-05,0.174921,0.0791124,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.000251928,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.000558597,0.253693,0.217069,0.190048,0.131088,0.090504,0.000180174,0.00501606,0.0761239,0.172491,0.0818785,0.182701,0.00836526,0.011488,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.000381649,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.153605,0.000122353,0.0255266,0.0465945,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.911304,0.00217769,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.00921075,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.0203723,0.218271,0.00534625,3.8251e-06,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.000797393,0.155821,0.0718905,0.0919008,0.0602373,0.0109522,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.0282663,0.251466,0.288096,0.00738316,0.0838874,0.331451,0.113145,0.000260208,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.00352872,0.103667,0.113069,0.025556,0.0149597,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.0546539,0.0362615,0.0590944,0.00309372,0.178389,0.218229,1.36398e-08,0.0161946,0.619906,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.0177337,0.36927,3.74842e-05,0.407369,0.231447,0.18653,0.0210947,0.37006,0.10748,0.00327292,0.197484,0.396996,0.36145,0.406019,0.0841307,0.057779,0.0863135,0.432035,0.722159,0.390366,0.48809,0.50058,0.443185,0.169835,0.3468,0.0572701,0.227104,0.166658,0.250246,0.0135352,0.284625,0.00583062,0.04783,0.144318,0.00513616,0.164197,0.462688,0.287881,0.574635,0.138768,0.336276,0.468444,0.258219,0.446557,0.243383,0.191695,0.0889613,0.149257,0.683217,0.161598,0.751174,0.000709044,0.0323708,0.476802,0.0805771,0.200632,0.477353,0.199161,0.746954,0.771991,0.20342,0.200493,0.20558,0.300504,0.00348292,0.425963,0.349197,0.383291,0.156104,0.141318,0.000226517,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,2.64048e-05,0.0513026,0.314429,0.00115141,0.282286,0.0192486,0.616388,0.408413,0.0374737,0.322213,0.00012402,0.33942,0.243065,0.0136291,0.522605,0.802166,0.000151141,0.222037,0.0175112,0.416292,0.462712,0.734551,0.0118519,0.204817,0.0233392,0.138871,0.103502,0.166905,0.19783,0.0833851,0.316453,0.0289164,0.175199,2.48419e-07,0.0120568,0.170369,0.000216517,0.0768488,0.534741,0.000165487,7.9815e-06,0.236011,0.203486,0.273398,0.375787,0.119167,9.87992e-10,0.275347,0.019895,2.40882e-06,0.241132,0.371414,0.30666,0.303709,0.0323359,0.0135408,0.508064,0.250964,0.383276,4.34235e-05,0.504711,0.0262575,0.0355483,0.196976,0.191517,0.0254647,0.0663581,0.307334,0.0246928,0.0048173,0.563586,0.472935,0.399569,0.273281,0.0114705,0.275089,0.0858306,1.20954e-10,0.0740334,0.339729,0.197805,5.57217e-05,0.0136044,0.332774,0.52832,0.299887,0.266492,0.205413,0.17639,0.0779009,0.0424553,0.022685,0.0337138,0.18966,0.258854,2.76616e-06,0.0719199,0.264884,0.162568,0.0195357,0.163057,0.00210664,0.208013,0.0900729,0.0953646,0.166124,0.0348699,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.00651011,0.0257082,0.0211771,0.186804,0.123324,0.199468,5.91485e-06,0.0933115,0.000350724,0.179889,0.0023439,0.27872,0.0855609,0.131118,0.20837,0.00021756,0.222339,0.0673329,0.20847,0.266544,0.000263373,0.145701,0.000156202,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.0363723,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,1.667e-05,0.00166408,0.21382,0.00176424,0.141867,0.00140109,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.0102599,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,8.4053e-05,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.0025753,6.87647e-05,0.0812887,0.0981146,0.064145,0.000332324,0.0638699,1.25159e-07,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,1.91331e-06,0.286691,0.3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}}
}}

Revision as of 15:16, 19 October 2012


Full id: C3624_cerebellum_serous_papillary_Renal_signet_teratocarcinoma_osteosarcoma



Phase1 CAGE Peaks

Hg19::chr17:35293932..35293947,-p2@ENST00000529264
Hg19::chr17:35293950..35293973,-p1@ENST00000528383
p1@ENST00000529264
p1@ENST00000532387
Hg19::chr17:35294075..35294102,+p7@LHX1


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
kidney tubule cell4.40e-1810
nephron tubule epithelial cell4.40e-1810
epithelial cell of nephron1.08e-1515
kidney cell1.99e-1317
kidney epithelial cell1.99e-1317
kidney cortical cell5.28e-1112
renal cortical epithelial cell5.28e-1112
epithelial cell1.32e-09253
Uber Anatomy
Ontology termp-valuen
cavitated compound organ4.72e-2431
kidney1.48e-2226
kidney mesenchyme1.48e-2226
upper urinary tract1.48e-2226
kidney rudiment1.48e-2226
kidney field1.48e-2226
nephron tubule epithelium4.40e-1810
excretory tube6.94e-1716
kidney epithelium6.94e-1716
nephron epithelium1.08e-1515
renal tubule1.08e-1515
nephron tubule1.08e-1515
nephron1.08e-1515
uriniferous tubule1.08e-1515
nephrogenic mesenchyme1.08e-1515
posterior neural tube2.23e-1415
chordal neural plate2.23e-1415
segmental subdivision of hindbrain3.70e-1312
hindbrain3.70e-1312
presumptive hindbrain3.70e-1312
trunk region element2.31e-12101
urinary system structure3.63e-1247
segmental subdivision of nervous system6.06e-1213
compound organ7.19e-1268
renal system8.88e-1248
cortex of kidney5.28e-1112
renal parenchyma5.28e-1112
abdomen element6.99e-1154
abdominal segment element6.99e-1154
cortex2.50e-1015
brainstem3.10e-106
regional part of metencephalon3.28e-099
metencephalon3.28e-099
future metencephalon3.28e-099
abdominal segment of trunk3.80e-0960
abdomen3.80e-0960
parenchyma2.34e-0815
central nervous system1.86e-0781
organ3.10e-07503
brain9.03e-0768
future brain9.03e-0768
Disease
Ontology termp-valuen
carcinoma6.76e-10106
cell type cancer1.17e-09143
cancer7.93e-09235
disease of cellular proliferation2.40e-08239


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)

{{{tfbs_overrepresentation_jaspar}}}



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
E2F6#187635.017155731697390.00791769806886330.0321669766450389
NFYB#4801316.75979325353650.0002123649923296180.00245535120490568



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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