FF:10616-108G4: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |F5samples= | ||
| | |ancestors_in_anatomy_facet= | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548 | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548 | ||
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:1749,DOID:305,DOID:4 | |ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:1749,DOID:305,DOID:4 | ||
| | |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:10616-108G4 | |||
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102024 | |is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102024 | ||
|name=squamous cell carcinoma cell line:T3M-5 | |||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan=,,, | |||
|profile_hcage=CNhs11739,LSID819,release009,COMPLETED | |||
|profile_rnaseq=,,, | |||
|profile_srnaseq=,,, | |||
|rna_box=108 | |||
|rna_catalog_number= | |||
|rna_concentration=0.83202 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |||
|rna_lot_number= | |||
|rna_od260/230=2.13 | |||
|rna_od260/280=2.1 | |||
|rna_position=G4 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=108G4 | |||
|rna_weight_ug=39.10494 | |||
|sample_age=71 | |||
|sample_cell_catalog=RCB1012 | |||
|sample_cell_line=T3M-5 | |||
|sample_cell_lot= | |||
|sample_cell_type=unclassifiable | |||
|sample_collaboration=Yukio Nakamura (RIKEN BRC) | |||
|sample_company=RIKEN Bioresource centre | |||
|sample_description= | |||
|sample_dev_stage= | |||
|sample_disease=squamous cell carcinoma | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity=J | |||
|sample_experimental_condition= | |||
|sample_id=10616 | |||
|sample_note= | |||
|sample_sex=female | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=thyroid | |||
|top_motifs=ELK1,4_GABP{A,B1}:2.20699747775;TP53:1.64690689655;POU1F1:1.51214667929;ZEB1:1.3937975203;POU2F1..3:1.3313972956;bHLH_family:1.16923940776;VSX1,2:1.03627752038;SNAI1..3:1.00694729207;ONECUT1,2:1.0068024684;TBX4,5:0.98830854121;BACH2:0.906408023434;ARID5B:0.890436894487;TEF:0.867396002379;TLX2:0.852685414825;FOSL2:0.834576024737;FOXQ1:0.815283922985;GLI1..3:0.796792583696;FOS_FOS{B,L1}_JUN{B,D}:0.775603246037;MYOD1:0.754732347822;PPARG:0.741005526116;ELF1,2,4:0.650800929978;POU6F1:0.593314014355;FOXD3:0.547828380745;ADNP_IRX_SIX_ZHX:0.523979442044;POU3F1..4:0.516440455831;HLF:0.467374322651;NFE2:0.465831631254;SOX17:0.462351674904;IKZF1:0.444294961848;ZBTB6:0.437364186017;TEAD1:0.428411357327;NKX2-1,4:0.417154116209;FOXM1:0.401205275667;HOXA9_MEIS1:0.399076222244;TBP:0.362016135754;HOX{A6,A7,B6,B7}:0.347953635309;PITX1..3:0.345542291976;LEF1_TCF7_TCF7L1,2:0.342138612558;FOXN1:0.319522074682;RBPJ:0.306087779687;HOX{A4,D4}:0.258786365974;OCT4_SOX2{dimer}:0.204972078323;NANOG:0.197451266859;NKX3-1:0.196268199665;NKX3-2:0.193916633732;PAX2:0.191059645706;ZBTB16:0.165239440408;ALX1:0.162223496661;LMO2:0.127023136019;GFI1:0.106085404479;PDX1:0.104736224694;TFDP1:0.0890169554498;NFIX:0.0865751720597;STAT5{A,B}:0.0860859160913;ATF4:0.0751152990267;PAX1,9:0.070735850862;ZNF143:0.0677370820329;ATF5_CREB3:0.0568815228559;FOX{F1,F2,J1}:0.0554853737149;HES1:0.0477668763483;IRF7:0.0390697745766;PRDM1:0.0349445901041;SPZ1:0.0341057989097;NFKB1_REL_RELA:0.0108199514261;GZF1:0.00172625731213;CRX:-0.00327923785429;AIRE:-0.00526347873271;AR:-0.00709413732587;CEBPA,B_DDIT3:-0.0155953317827;TFAP2{A,C}:-0.0164717589512;CDC5L:-0.039870736456;GTF2A1,2:-0.0659185948281;FOXA2:-0.0760936636707;ZNF148:-0.0823514925837;T:-0.0847885670641;CREB1:-0.0877646710835;NFIL3:-0.103804373331;ATF2:-0.116718830473;GATA6:-0.130188155028;AHR_ARNT_ARNT2:-0.139828582475;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.140462926885;SMAD1..7,9:-0.141078706786;PAX8:-0.143820581616;EN1,2:-0.144020863817;PAX4:-0.147931007804;TLX1..3_NFIC{dimer}:-0.159190221946;ATF6:-0.165240031047;REST:-0.168339711222;ETS1,2:-0.173761113614;GFI1B:-0.177450972997;MTF1:-0.180030587416;TFCP2:-0.180432096119;YY1:-0.227184053207;XCPE1{core}:-0.270059076654;FOXP1:-0.273640878882;NR1H4:-0.274500790996;UFEwm:-0.276183910742;CDX1,2,4:-0.277727261441;RFX2..5_RFXANK_RFXAP:-0.283073895326;SPI1:-0.287070677963;NFY{A,B,C}:-0.287575742421;HNF1A:-0.288850682003;DMAP1_NCOR{1,2}_SMARC:-0.302768302244;FOX{D1,D2}:-0.306312936222;FOX{I1,J2}:-0.330916788912;HIC1:-0.334404059626;NR6A1:-0.336077199773;NHLH1,2:-0.343797343235;ZFP161:-0.348303270891;MYBL2:-0.357858522228;MED-1{core}:-0.368096449745;RFX1:-0.375797884352;ZIC1..3:-0.381599444697;PRRX1,2:-0.389014732211;SP1:-0.393380866504;TOPORS:-0.40034252857;MEF2{A,B,C,D}:-0.402513421254;E2F1..5:-0.40898966897;SPIB:-0.424408344657;HOX{A5,B5}:-0.432115969847;SOX{8,9,10}:-0.434014419407;IRF1,2:-0.435253618494;KLF4:-0.454950261388;EP300:-0.471029584882;NFE2L2:-0.475849714813;XBP1:-0.488116551441;MYB:-0.49328612538;JUN:-0.506663730196;NRF1:-0.5104834559;SRF:-0.511349755147;LHX3,4:-0.524349675333;EGR1..3:-0.537542864007;NKX2-2,8:-0.539616288777;NKX2-3_NKX2-5:-0.54084244149;MTE{core}:-0.548816687959;TFAP2B:-0.584919409379;PAX6:-0.601846431291;ZNF423:-0.602879224337;TFAP4:-0.621902720699;SOX2:-0.622273928688;BPTF:-0.623050907503;HNF4A_NR2F1,2:-0.627649150688;GTF2I:-0.645545986713;PBX1:-0.647241173534;EVI1:-0.657698210348;CUX2:-0.661619275701;RORA:-0.663096765488;ESR1:-0.67211617827;BREu{core}:-0.680342647361;PAX5:-0.691741315441;FOXL1:-0.694615499685;HBP1_HMGB_SSRP1_UBTF:-0.698234781805;POU5F1:-0.700780254215;HAND1,2:-0.70849225329;HIF1A:-0.715262522038;MAFB:-0.718086421628;STAT2,4,6:-0.736022693726;FOXO1,3,4:-0.778720975387;RXR{A,B,G}:-0.780287298299;PAX3,7:-0.783224689557;MYFfamily:-0.785537609176;TAL1_TCF{3,4,12}:-0.788858735175;DBP:-0.826869825777;RUNX1..3:-0.831945183179;GCM1,2:-0.843929309452;NFATC1..3:-0.855842162468;SREBF1,2:-0.865961148587;MAZ:-0.907761457793;HMGA1,2:-0.935177156742;NR3C1:-0.943628756756;ZNF384:-0.975768954968;IKZF2:-0.984229707559;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.991059119653;NKX6-1,2:-1.009375593;NR5A1,2:-1.03510866895;TGIF1:-1.04520899516;ALX4:-1.08902631381;PATZ1:-1.12125727086;STAT1,3:-1.13003903238;EBF1:-1.19016849318;HSF1,2:-1.19414273825;RREB1:-1.22831493838;SOX5:-1.27099482947;ZNF238:-1.28042972054;NFE2L1:-1.3151860105;GATA4:-1.32146343781;RXRA_VDR{dimer}:-1.39731661232;NANOG{mouse}:-1.46759813414;HMX1:-1.5174585526;MZF1:-1.52139571826;ESRRA:-1.65567376086;FOXP3:-1.81382814498 | |||
}} | }} |
Revision as of 14:11, 21 March 2012
Name: | squamous cell carcinoma cell line:T3M-5 |
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Species: | Human (Homo sapiens) |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
ExpandAdditional information |
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ExpandDownload 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: CNhs11739
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: CNhs11739
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: CNhs11739
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
FF:0102024 squamous cell carcinoma cell line sample
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)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
1749 (squamous cell carcinoma)
305 (carcinoma)
4 (disease)
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