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{{f5samples
{{f5samples
|id=FF:10285-104F6
|F5samples=
|name=Skin - cornified area on sole of foot, donor1
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000026,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000154,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001048,UBERON:0001062,UBERON:0001419,UBERON:0001513,UBERON:0002050,UBERON:0002097,UBERON:0002101,UBERON:0002103,UBERON:0002199,UBERON:0002387,UBERON:0002416,UBERON:0002470,UBERON:0002529,UBERON:0002532,UBERON:0003081,UBERON:0003102,UBERON:0003532,UBERON:0004120,UBERON:0004347,UBERON:0004357,UBERON:0004708,UBERON:0004709,UBERON:0005423,UBERON:0005732,UBERON:0005733,UBERON:0007023,UBERON:0008784
|sample_id=10285
|rna_tube_id=
|rna_box=104
|rna_position=F6
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=1-Sk5
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=Skin - cornified area on sole of foot
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=
|sample_ethnicity=
|rna_rin=2.40000
|rna_od260/230=1.64000
|rna_od260/280=2.08000
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=Alessandro Bonetti
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=25.22232
|rna_concentration=
|sample_note=
|profile_hcage=,LSID1024,,SEQUENCING QUEUE
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000026,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000154,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001048,UBERON:0001062,UBERON:0001419,UBERON:0001513,UBERON:0002050,UBERON:0002097,UBERON:0002101,UBERON:0002103,UBERON:0002199,UBERON:0002387,UBERON:0002416,UBERON:0002470,UBERON:0002529,UBERON:0002532,UBERON:0003081,UBERON:0003102,UBERON:0003532,UBERON:0004120,UBERON:0004347,UBERON:0004357,UBERON:0004708,UBERON:0004709,UBERON:0005423,UBERON:0005732,UBERON:0005733,UBERON:0007023,UBERON:0008784
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 34:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10285-104F6
|is_a=EFO:0002091;;FF:0011176
|is_a=EFO:0002091;;FF:0011176
|name=Skin - cornified area on sole of foot, donor1
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=,LSID1024,,SEQUENCING QUEUE
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=104
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=1-Sk5
|rna_od260/230=1.64000
|rna_od260/280=2.08000
|rna_position=F6
|rna_rin=2.40000
|rna_sample_type=total RNA
|rna_tube_id=
|rna_weight_ug=25.22232
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=Alessandro Bonetti
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10285
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=Skin - cornified area on sole of foot
|top_motifs=MEF2{A,B,C,D}:6.72309461687;NR1H4:5.16554909008;PDX1:4.19504708447;POU1F1:4.12793258191;ESRRA:3.87482280414;NKX2-2,8:3.83922942473;NR5A1,2:3.49318913746;AR:3.28909184501;FOXL1:3.26998738635;NFE2L1:3.20582558815;STAT5{A,B}:3.0635169373;IKZF2:3.05829334468;NR6A1:2.88137821578;ZBTB16:2.79100457146;NFIX:2.75592437805;HOX{A4,D4}:2.69447312042;HAND1,2:2.60848391419;MYOD1:2.53472211712;TGIF1:2.51183156249;EVI1:2.47747939076;POU6F1:2.27485747187;MAFB:2.24094636828;SOX5:2.23400057223;PAX4:2.12770821377;RXR{A,B,G}_{NR1H2,PPAR}dimers:2.11252291852;CUX2:2.11197746708;GLI1..3:2.11125077364;GATA4:2.10596065012;SPZ1:2.10123685398;RORA:2.07539693425;FOXQ1:2.06009075386;RXR{A,B,G}:1.95311005253;ALX1:1.85778544604;SMAD1..7,9:1.84946087821;UFEwm:1.81539186947;PPARG:1.7907801437;SRF:1.7848646922;FOXP3:1.77455407151;YY1:1.7079816636;CDX1,2,4:1.67280699477;BPTF:1.65053019785;NKX6-1,2:1.58504909508;NHLH1,2:1.50974670332;ZNF384:1.4676109626;PITX1..3:1.36357525735;FOXO1,3,4:1.30114807262;KLF4:1.26430601791;HOX{A6,A7,B6,B7}:1.25991435839;PAX6:1.21748070318;POU3F1..4:1.17487648574;FOX{F1,F2,J1}:1.16283858559;NR3C1:1.14946620519;ATF2:1.09412740614;HSF1,2:1.09150154065;NKX3-2:1.03911421548;MYBL2:0.957374960619;FOXM1:0.956376315959;HMGA1,2:0.95605294038;ESR1:0.955007151894;TLX2:0.901160146807;FOX{D1,D2}:0.899300506086;NKX2-1,4:0.897077811645;RREB1:0.853677265257;NFATC1..3:0.790162225322;LMO2:0.723041861729;HES1:0.709965577327;LHX3,4:0.690142231552;LEF1_TCF7_TCF7L1,2:0.683107650058;EN1,2:0.602041781923;TFAP4:0.578177591836;PBX1:0.510890517848;XBP1:0.478229037064;RFX2..5_RFXANK_RFXAP:0.469921900611;GCM1,2:0.43314167227;SNAI1..3:0.425122607491;TFAP2{A,C}:0.40542651214;ONECUT1,2:0.393641660286;TEAD1:0.314126495221;HNF4A_NR2F1,2:0.300515833206;HIC1:0.29585807631;TOPORS:0.246281070036;CEBPA,B_DDIT3:0.24503984875;MTF1:0.243466510658;GTF2A1,2:0.236363388611;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.214820016805;ZIC1..3:0.200082620533;IRF7:0.185257820075;MED-1{core}:0.17854716316;TFCP2:0.130809113227;PATZ1:0.125270663284;ZFP161:0.105717050931;GFI1B:0.10389552589;PAX1,9:0.0883186234481;REST:0.0516052122402;TBP:0.0376242477565;FOXN1:0.0126398332567;ZEB1:-0.0441065735712;NANOG:-0.0653500114884;DMAP1_NCOR{1,2}_SMARC:-0.0778254887775;TFAP2B:-0.0931551223816;PAX2:-0.106072737552;TLX1..3_NFIC{dimer}:-0.111635084049;ARID5B:-0.116126931618;RBPJ:-0.127991245557;TBX4,5:-0.133129661548;ATF4:-0.146078011328;MTE{core}:-0.155905946418;ATF5_CREB3:-0.157628434327;HMX1:-0.188132020884;TAL1_TCF{3,4,12}:-0.199655001024;SOX17:-0.214923073732;MYFfamily:-0.227819776696;ALX4:-0.269880953632;ATF6:-0.277654379577;FOSL2:-0.277677653503;IKZF1:-0.294886005085;NKX2-3_NKX2-5:-0.299441636188;GTF2I:-0.30484813725;FOXP1:-0.314668262613;bHLH_family:-0.317506315628;EP300:-0.317897871614;ZBTB6:-0.329902243069;NFE2:-0.338726135499;STAT2,4,6:-0.350904279123;AIRE:-0.356149502933;SOX{8,9,10}:-0.375279532445;TP53:-0.406008105277;PRDM1:-0.410932412135;JUN:-0.413511324971;NKX3-1:-0.41844377017;ZNF143:-0.437612192479;PAX3,7:-0.463353644861;MAZ:-0.470408450147;ZNF423:-0.480543236037;MZF1:-0.485859815122;SREBF1,2:-0.487993506781;HLF:-0.498745716946;T:-0.507415030956;ETS1,2:-0.510848047454;FOXA2:-0.530894310374;ZNF238:-0.542143145452;HOX{A5,B5}:-0.543637282231;BREu{core}:-0.570828410285;TEF:-0.575503861309;GZF1:-0.584530713019;NFKB1_REL_RELA:-0.59519560296;CRX:-0.612812309351;SPI1:-0.625107686578;NFIL3:-0.636614003586;FOS_FOS{B,L1}_JUN{B,D}:-0.653499890824;AHR_ARNT_ARNT2:-0.662772351757;HNF1A:-0.664996880375;IRF1,2:-0.66649574437;EGR1..3:-0.683086065235;NRF1:-0.713124420629;OCT4_SOX2{dimer}:-0.717385841299;RXRA_VDR{dimer}:-0.760546308585;NFE2L2:-0.79702501086;BACH2:-0.800875054919;ZNF148:-0.801343127355;NANOG{mouse}:-0.806483183487;FOXD3:-0.822641076987;CREB1:-0.888220946824;GATA6:-0.901562734492;SPIB:-0.906742966291;PAX5:-1.06533480789;E2F1..5:-1.101706289;CDC5L:-1.13651772803;ELF1,2,4:-1.15403877485;ELK1,4_GABP{A,B1}:-1.27352657711;RUNX1..3:-1.30999449854;SP1:-1.398010708;HOXA9_MEIS1:-1.44068575881;STAT1,3:-1.45499762087;RFX1:-1.46991818231;HIF1A:-1.48598344161;TFDP1:-1.52088367811;NFY{A,B,C}:-1.57539138932;EBF1:-1.61779724191;DBP:-1.62047546719;ADNP_IRX_SIX_ZHX:-1.68778481736;SOX2:-1.72327863193;MYB:-1.82686130891;GFI1:-1.89493386389;HBP1_HMGB_SSRP1_UBTF:-1.95636876485;FOX{I1,J2}:-2.08785350091;POU5F1:-2.27442089538;PRRX1,2:-2.29420665344;POU2F1..3:-2.6006646115;PAX8:-2.63572132906;XCPE1{core}:-2.85128690838;VSX1,2:-3.11944693642
}}
}}

Revision as of 14:05, 21 March 2012


Name:Skin - cornified area on sole of foot, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueSkin - cornified area on sole of foot
dev stageNA
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationAlessandro Bonetti
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1-Sk5
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br>


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000014 (zone of skin)
0000026 (appendage)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000154 (posterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001048 (primordium)
0001062 (anatomical entity)
0001419 (skin of limb)
0001513 (skin of foot)
0002050 (embryonic structure)
0002097 (skin of body)
0002101 (limb)
0002103 (hindlimb)
0002199 (integument)
0002387 (foot)
0002416 (integumental system)
0002470 (autopod region)
0002529 (limb segment)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003102 (surface structure)
0003532 (hindlimb skin)
0004120 (mesoderm-derived structure)
0004347 (limb bud)
0004357 (paired limb/fin bud)
0004708 (paired limb/fin)
0004709 (pelvic appendage)
0005423 (developing anatomical structure)
0005732 (limb/fin field)
0005733 (limb field)
0007023 (adult organism)
0008784 (lower limb segment)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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