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Coexpression cluster:C4836: Difference between revisions

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|full_id=C4836_non_granulocyte_Melanocyte_amniotic_small_epitheloid_merkel
|full_id=C4836_non_granulocyte_Melanocyte_amniotic_small_epitheloid_merkel
|id=C4836
|id=C4836
|ontology_enrichment_celltype=CL:0000066!1.13e-08!254
|ontology_enrichment_celltype=CL:0000066!1.04e-07!253
|ontology_enrichment_disease=DOID:162!1.08e-38!235;DOID:14566!1.19e-37!239;DOID:0050687!6.31e-22!143;DOID:305!2.84e-19!106;DOID:0050686!3.27e-16!137;DOID:2531!3.18e-12!51;DOID:0060083!3.18e-12!51;DOID:1240!2.16e-09!39
|ontology_enrichment_disease=DOID:162!1.19e-35!235;DOID:14566!7.93e-35!239;DOID:0050687!1.42e-20!143;DOID:305!6.94e-18!106;DOID:0050686!4.63e-15!137;DOID:2531!1.16e-11!51;DOID:0060083!1.16e-11!51;DOID:1240!1.80e-08!39
|ontology_enrichment_uberon=UBERON:0001557!4.36e-07!19
|ontology_enrichment_uberon=UBERON:0001557!7.49e-07!19
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191439844704929!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00663294930729599!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0328289500568538!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00439525624637053!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324815959075345!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465443847535711!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00902717120171123!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.015495493492261!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00394074156952512!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128859157827173!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000254319272071778!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296514174048989!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00200369356903486!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246874303583181!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173796386567567!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00137474858485337!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00487033817494776!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278646373087087!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0248190176167158!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000943222789927745!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155470021880583!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00546384044426369!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191405328832014
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191439844704929!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00663294930729599!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0328289500568538!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00439525624637053!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324815959075345!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465443847535711!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00902717120171123!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.015495493492261!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00394074156952512!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128859157827173!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000254319272071778!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296514174048989!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00200369356903486!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246874303583181!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173796386567567!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00137474858485337!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00487033817494776!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278646373087087!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0248190176167158!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000943222789927745!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155470021880583!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00546384044426369!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191405328832014
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112557,0.222432,0.107043,0.0419304,0.00481323,0.173708,0.141119,0.0241568,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.000389382,6.05e-09,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0008845,0.0345419,0.0388736,0.00340073,0.170307,0.0015938,0.0488949,0.016278,0.0791124,0.0330727,0.00100273,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.00370214,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0015426,0.0109154,0.253693,0.00203513,0.00133367,0.131088,0.394069,0.0306378,1.17885e-10,0.0761239,0.172491,0.0818785,0.182701,0.00836526,0.147698,0.141463,0.167267,0.140622,0.0889592,0.00643528,0.0458479,0.00113687,0.094881,0.022113,0.00924871,3.55381e-10,0.109194,0.00864322,0.131452,0.323837,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.389379,0.655293,0.21727,0.289306,0.119215,0.192475,0.0168693,0.547859,0.057571,1.86293e-05,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.0271723,0.000444106,0.0355833,0.00824114,0.175094,0.0121461,0.00739585,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.00474777,0.00171529,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.0158019,0.104948,0.00217546,0.00166615,0.234298,7.75285e-05,0.0457643,2.72738e-05,0.194941,0.218271,0.101607,5.85104e-05,0.172982,0.340936,0.0121199,0.0626744,0.191335,0.0116284,0.000797393,0.155821,0.0718905,0.0919008,0.0602373,0.0109522,0.0119616,0.0973823,0.0126914,0.170295,0.193653,0.137219,0.228144,0.251466,0.0461822,0.000308572,0.00362128,0.331451,0.113145,0.000260208,0.186638,0.00102368,3.7942e-06,0.264079,0.00316392,0.140533,0.000178916,7.51964e-07,0.103667,0.113069,0.025556,1.19804e-09,0.09066,0.220462,0.166967,0.188651,9.56941e-05,0.184948,3.03264e-05,0.311847,0.0362615,0.0590944,0.247324,5.31e-05,0.218229,0.231073,0.000211542,0.0170505,0.0360851,0.412187,0.000416337,0.0434602,0.133616,0.418146,0.0115948,0.449036,0.407369,0.231447,0.00858901,0.0210947,0.37006,0.10748,0.022688,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.643768,0.432035,0.722159,0.0140037,0.48809,0.153829,0.443185,0.522904,0.158867,0.00127936,0.227104,0.00667974,0.0734371,0.38649,0.00488219,0.00583062,0.55194,0.729153,0.0465139,0.164197,4.69946e-05,0.287881,0.00187974,0.0283889,0.336276,0.468444,0.258219,0.446557,0.243383,0.191695,0.0889613,0.73485,0.029557,0.161598,0.0527155,0.000709044,0.00534461,0.0239796,0.0120582,0.0704414,0.477353,0.0201095,0.746954,0.000852086,0.20342,0.200493,0.20558,0.00583368,7.31928e-07,0.425963,0.349197,0.0851996,0.156104,0.141318,0.411941,0.00477789,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.0674279,0.616388,0.0978616,0.516511,0.0073454,0.656109,0.33942,0.61031,0.0136291,0.522605,0.0248202,0.180745,0.222037,0.416621,0.416292,0.462712,0.734551,0.0019893,0.00169113,0.452428,0.138871,0.103502,0.166905,0.19783,0.0833851,0.316453,0.140384,0.175199,0.332919,0.373557,0.170369,0.408861,0.365487,0.00780726,0.0889149,0.363192,0.236011,0.203486,0.273398,0.0123025,0.119167,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.0131557,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.0517073,0.0272975,0.0151656,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.0406989,0.299887,0.634365,0.205413,0.17639,0.0779009,0.0424553,0.205298,0.0337138,0.18966,0.258854,0.0189519,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.0828367,0.255516,0.20753,0.447185,0.00111175,0.193601,0.220904,0.222977,0.341681,0.00651011,0.21801,0.198614,0.186804,0.123324,0.0213665,0.0325925,0.0933115,3.04194e-07,0.00112112,0.226869,0.27872,0.0855609,0.131118,0.0233967,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.0218443,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.00113527,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.0159159,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,1.5182e-07,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.000677683,0.261724,0.211332,0.187731,0.0297055,6.87647e-05,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.000206969,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.00553696,0.286691,0.00940743,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,6.75665e-07,0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}}
}}

Revision as of 16:17, 19 October 2012


Full id: C4836_non_granulocyte_Melanocyte_amniotic_small_epitheloid_merkel



Phase1 CAGE Peaks

Hg19::chr9:99180597..99180614,-p3@ZNF367
Hg19::chr9:99180617..99180658,-p1@ZNF367
Hg19::chr9:99180662..99180690,-p2@ZNF367


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 cell1.04e-07253
Uber Anatomy
Ontology termp-valuen
upper respiratory tract7.49e-0719
Disease
Ontology termp-valuen
cancer1.19e-35235
disease of cellular proliferation7.93e-35239
cell type cancer1.42e-20143
carcinoma6.94e-18106
organ system cancer4.63e-15137
hematologic cancer1.16e-1151
immune system cancer1.16e-1151
leukemia1.80e-0839


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
CCNT2#90536.336201576962630.003930750035764890.0191439844704929
CHD2#1106310.34402283411690.0009033701102746880.00663294930729599
E2F1#186934.907389214879320.008460985347239390.0328289500568538
E2F4#1874312.66806031528440.0004917987006298980.00439525624637053
E2F6#187635.017155731697390.00791769806886330.0324815959075345
ELF1#199734.258097958807540.01295179875054610.0465443847535711
FOS#235338.99795530889440.001372499272417130.00902717120171123
GABPB1#255337.067683836182170.002832212825417420.015495493492261
HDAC2#3066313.41562023662630.0004140761399857210.00394074156952512
IRF1#365937.63716375356390.002244692747297240.0128859157827173
IRF3#3661346.98195221148969.63568551583244e-060.000254319272071778
MYC#460935.22228187160940.007020843755740150.0296514174048989
NFYA#4800318.42558069983050.0001598135507814160.00200369356903486
NFYB#4801316.75979325353650.0002123649923296180.00246874303583181
PAX5#507936.669565531177830.003370290999677260.0173796386567567
PBX3#5090321.91451268674419.49854535978121e-050.00137474858485337
RFX5#5993312.04791082719510.0005717246050312580.00487033817494776
SIN3A#2594235.408884726815140.006318961977991520.0278646373087087
SP1#666735.69838137814090.005403962701712170.0248190176167158
SP2#6668326.15353049384465.58768218891694e-050.000943222789927745
STAT1#6772320.70658749719920.0001125992441046670.00155470021880583
TAF7#6879311.43306940492390.0006690181981945830.00546384044426369
USF1#739136.361499277207960.00388404057290560.0191405328832014



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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