FF:10702-109G9: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |F5samples= | ||
| | |ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0001062,UBERON:0002097,UBERON:0002199,UBERON:0002416,UBERON:0003102 | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548 | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548 | ||
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:0060122,DOID:14566,DOID:162,DOID:2513,DOID:305,DOID:3451,DOID:4,DOID:4159 | |ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:0060122,DOID:14566,DOID:162,DOID:2513,DOID:305,DOID:3451,DOID:4,DOID:4159 | ||
| | |comment= | ||
|created_by= | |||
|creation_date= | |||
|def= | |||
|fonse_cell_line=FF:0101120 | |fonse_cell_line=FF:0101120 | ||
|fonse_cell_line_closure=FF:0101120 | |fonse_cell_line_closure=FF:0101120 | ||
Line 66: | Line 34: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|id=FF:10702-109G9 | |||
|is_a=DOID:2513;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100297;;UBERON:0000014 | |is_a=DOID:2513;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100297;;UBERON:0000014 | ||
|name=basal cell carcinoma cell line:TE 354.T | |||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan=,,, | |||
|profile_hcage=CNhs11932,LSID835,release010,COMPLETED | |||
|profile_rnaseq=,,, | |||
|profile_srnaseq=,,, | |||
|rna_box=109 | |||
|rna_catalog_number= | |||
|rna_concentration=0.2085 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |||
|rna_lot_number= | |||
|rna_od260/230=1.22 | |||
|rna_od260/280=2.05 | |||
|rna_position=G9 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=109G9 | |||
|rna_weight_ug=5.6295 | |||
|sample_age= | |||
|sample_cell_catalog=CRL-7762 | |||
|sample_cell_line=TE 354.T | |||
|sample_cell_lot= | |||
|sample_cell_type=unclassifiable | |||
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest) | |||
|sample_company=ATCC | |||
|sample_description= | |||
|sample_dev_stage= | |||
|sample_disease=basal cell carcinoma | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity= | |||
|sample_experimental_condition= | |||
|sample_id=10702 | |||
|sample_note= | |||
|sample_sex=female | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=skin | |||
|top_motifs=HMGA1,2:2.50257335401;MYBL2:2.27554316273;EVI1:2.17167518789;HIF1A:1.97791784878;UFEwm:1.97239731939;XBP1:1.96966777481;ESR1:1.82565775745;ALX4:1.77242285506;GCM1,2:1.67093512387;SRF:1.65065320566;AIRE:1.57502839743;FOXL1:1.53078281748;GLI1..3:1.46724466396;NR3C1:1.46074883681;NKX3-2:1.33312069505;TP53:1.33029405149;TAL1_TCF{3,4,12}:1.28095576845;POU3F1..4:1.2421602752;NKX2-2,8:1.2372162244;NFATC1..3:1.19121091261;HMX1:1.17619570732;TEAD1:1.14012192015;PAX8:1.13936744022;NKX3-1:1.10436895524;FOX{I1,J2}:1.07207451219;ATF6:1.0636469366;KLF4:1.06201463201;IKZF1:1.01588021193;ZBTB6:0.945597782282;GATA4:0.943941839866;TFCP2:0.939869449547;GTF2A1,2:0.939807026718;MAFB:0.911890604353;GZF1:0.903149578907;LHX3,4:0.892996857394;PPARG:0.884849419535;NFIX:0.870787896345;ZIC1..3:0.86214049168;PAX4:0.848643369513;HOX{A5,B5}:0.825038785599;HES1:0.822572758249;SOX17:0.796513058202;POU1F1:0.750064585237;EBF1:0.739616053142;NFE2L1:0.736601843741;HOX{A4,D4}:0.731513273512;PRDM1:0.724852146628;EN1,2:0.704182173571;SPZ1:0.686024445654;XCPE1{core}:0.655477685677;ARID5B:0.636198954084;STAT5{A,B}:0.635237905594;TEF:0.606411857668;HBP1_HMGB_SSRP1_UBTF:0.600033251032;HLF:0.593076038339;HAND1,2:0.569493741557;NFE2L2:0.569443073726;NKX2-1,4:0.551802561547;MAZ:0.526256570541;ZBTB16:0.522795438855;MTE{core}:0.521788847091;TFAP4:0.510783961417;RXRA_VDR{dimer}:0.503603583955;ZNF384:0.497201859926;FOXM1:0.480229762358;FOXO1,3,4:0.476757980711;RXR{A,B,G}:0.439648389723;GTF2I:0.38998128158;TBX4,5:0.385636913963;TLX1..3_NFIC{dimer}:0.373535812166;TFAP2B:0.363964355146;EP300:0.350985423591;TBP:0.344067778647;FOXA2:0.343549707312;ZNF148:0.342912535152;AHR_ARNT_ARNT2:0.292495482869;STAT2,4,6:0.262510148887;NANOG{mouse}:0.255910374341;CDC5L:0.253714780622;ZNF238:0.242645963536;MEF2{A,B,C,D}:0.240310550266;HSF1,2:0.235715368705;TFAP2{A,C}:0.230080193404;GFI1B:0.213085509871;ONECUT1,2:0.198314781308;ADNP_IRX_SIX_ZHX:0.19671992867;HIC1:0.132046031467;FOXD3:0.129162273668;LEF1_TCF7_TCF7L1,2:0.117524980165;AR:0.104780450525;PAX1,9:0.0548878926735;NR6A1:0.0322649083158;SP1:0.0213946450874;FOSL2:0.0131194778857;FOS_FOS{B,L1}_JUN{B,D}:-0.0193352438027;BACH2:-0.0234436440162;DBP:-0.0451025238794;IRF1,2:-0.0950721492203;MZF1:-0.0955748788816;MYFfamily:-0.0968601064042;JUN:-0.102330956194;PAX3,7:-0.111596372614;FOXP3:-0.118725003988;RUNX1..3:-0.145305594256;TFDP1:-0.150481638699;REST:-0.16080684605;T:-0.172524287317;ZFP161:-0.174986627816;BPTF:-0.175815533586;PAX6:-0.179596223589;NFE2:-0.232133426451;MYB:-0.241361078538;PATZ1:-0.252530773462;NHLH1,2:-0.255131700932;POU6F1:-0.266554086838;EGR1..3:-0.267828063173;DMAP1_NCOR{1,2}_SMARC:-0.294550789624;PAX5:-0.301239284471;NFKB1_REL_RELA:-0.301359364037;NFIL3:-0.30438644693;ESRRA:-0.318030884553;bHLH_family:-0.318106366156;NKX2-3_NKX2-5:-0.318701508688;HNF1A:-0.328675294935;POU5F1:-0.354301592275;CREB1:-0.355912655232;PAX2:-0.364558851919;RFX1:-0.371600886209;TGIF1:-0.378103826513;FOX{D1,D2}:-0.384715511015;FOXN1:-0.38512619203;SMAD1..7,9:-0.387103840998;RREB1:-0.400372099317;HOXA9_MEIS1:-0.403670102738;ZNF423:-0.407065016815;TOPORS:-0.408933023253;LMO2:-0.41416709081;ATF2:-0.421923994197;NR5A1,2:-0.457218499739;SNAI1..3:-0.464471253876;NRF1:-0.464822772914;CEBPA,B_DDIT3:-0.479536997081;MED-1{core}:-0.485845457079;ZNF143:-0.488294845007;YY1:-0.509667403529;PRRX1,2:-0.513618561995;ELK1,4_GABP{A,B1}:-0.517633419091;OCT4_SOX2{dimer}:-0.523959739436;SPI1:-0.566850910646;ETS1,2:-0.578307420149;FOX{F1,F2,J1}:-0.598118141969;ZEB1:-0.600370980695;VSX1,2:-0.60618286853;RORA:-0.61701558957;FOXP1:-0.625406934713;ATF5_CREB3:-0.636628408689;FOXQ1:-0.641200568241;PITX1..3:-0.680810641736;HOX{A6,A7,B6,B7}:-0.690372017742;GFI1:-0.696932453979;SPIB:-0.701755867525;HNF4A_NR2F1,2:-0.704860895989;ATF4:-0.75865155703;SOX2:-0.759593131511;SOX5:-0.762957026238;GATA6:-0.763524010554;PDX1:-0.777824995073;ELF1,2,4:-0.843651031098;IRF7:-0.854994971999;NANOG:-0.870362737591;CUX2:-0.873960709579;BREu{core}:-0.887254012153;CDX1,2,4:-0.894978813523;E2F1..5:-0.926687492413;IKZF2:-0.930212423375;SREBF1,2:-0.954178804674;NR1H4:-0.978182064974;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.982201971767;MYOD1:-0.982840960482;MTF1:-1.00530990061;TLX2:-1.04577851701;STAT1,3:-1.07225573634;RFX2..5_RFXANK_RFXAP:-1.12296108088;CRX:-1.13227417014;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.18860900509;POU2F1..3:-1.23017386085;NKX6-1,2:-1.28297169302;ALX1:-1.35563915596;SOX{8,9,10}:-1.42850125214;NFY{A,B,C}:-1.45116593142;PBX1:-1.48137655607;RBPJ:-1.73623536108 | |||
}} | }} |
Revision as of 14:13, 21 March 2012
Name: | basal cell carcinoma cell line:TE 354.T |
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Species: | Human (Homo sapiens) |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
Additional information | ||||||||||||||||||||||||||||
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Sample information
RNA information
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Download raw sequence, BAM & CTSS | ||||||||||||
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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
library id: CNhs11932
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
library id: CNhs11932
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>
library id: CNhs11932
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
DOID:2513 basal cell carcinoma
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
FF:0100297 carcinoma cell line sample
UBERON:0000014 zone of skin
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
CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
0060122 (integumentary system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2513 (basal cell carcinoma)
305 (carcinoma)
3451 (skin carcinoma)
4 (disease)
4159 (skin cancer)
UBERON: Anatomy
0000014 (zone of skin)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0001062 (anatomical entity)
0002097 (skin of body)
0002199 (integument)
0002416 (integumental system)
0003102 (surface structure)
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