FF:10726-110A6: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |F5samples= | ||
| | |ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet=DOID:0050687,DOID:1115,DOID:14566,DOID:162,DOID:4 | |ancestors_in_disease_facet=DOID:0050687,DOID:1115,DOID:14566,DOID:162,DOID:4 | ||
| | |comment= | ||
|created_by= | |||
|creation_date= | |||
|def= | |||
|fonse_cell_line=FF:0100400 | |fonse_cell_line=FF:0100400 | ||
|fonse_cell_line_closure=FF:0100400 | |fonse_cell_line_closure=FF:0100400 | ||
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|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|id=FF:10726-110A6 | |||
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0103743 | |is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0103743 | ||
|name=liposarcoma cell line:SW 872 | |||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan=,,, | |||
|profile_hcage=CNhs11851,LSID830,release010,COMPLETED | |||
|profile_rnaseq=,,, | |||
|profile_srnaseq=,,, | |||
|rna_box=110 | |||
|rna_catalog_number= | |||
|rna_concentration=0.83412 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |||
|rna_lot_number= | |||
|rna_od260/230=2.11 | |||
|rna_od260/280=2.1 | |||
|rna_position=A6 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=110A6 | |||
|rna_weight_ug=22.52124 | |||
|sample_age=36 | |||
|sample_cell_catalog=HTB-92 | |||
|sample_cell_line=SW 872 | |||
|sample_cell_lot= | |||
|sample_cell_type=adipocyte | |||
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest) | |||
|sample_company=ATCC | |||
|sample_description= | |||
|sample_dev_stage= | |||
|sample_disease=liposarcoma | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity=C | |||
|sample_experimental_condition= | |||
|sample_id=10726 | |||
|sample_note= | |||
|sample_sex=male | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=unclassifiable | |||
|top_motifs=TFDP1:1.500209646;XCPE1{core}:1.49718077467;SP1:1.24770658547;TLX1..3_NFIC{dimer}:1.1619344578;GFI1:1.08473858341;NFY{A,B,C}:1.02401609878;PATZ1:1.00821904393;E2F1..5:0.930689129154;TFAP2B:0.897710859837;FOX{I1,J2}:0.885279610276;RBPJ:0.876520027886;PRRX1,2:0.774730946465;NRF1:0.763146078333;EN1,2:0.758990460004;STAT1,3:0.708478620503;EGR1..3:0.698379385194;BREu{core}:0.673608685485;HIC1:0.654808210263;PBX1:0.628971108111;RFX1:0.584774050275;RXR{A,B,G}:0.558296336632;CDX1,2,4:0.558183422172;MED-1{core}:0.541398239642;HOX{A6,A7,B6,B7}:0.530338165149;bHLH_family:0.524404284646;PAX8:0.506613945595;HOX{A5,B5}:0.468305422131;ZNF143:0.462005758018;PAX6:0.461650748065;IRF1,2:0.455220673776;ELK1,4_GABP{A,B1}:0.45502261028;PPARG:0.419557163004;PAX1,9:0.395916455986;ZFP161:0.383758896621;RORA:0.374042833553;HES1:0.371661236771;NKX2-3_NKX2-5:0.369391822725;SOX17:0.364894763895;PAX5:0.363418217595;MTE{core}:0.347298925058;GTF2A1,2:0.340852811803;FOX{D1,D2}:0.310108377612;CDC5L:0.295523192121;TEF:0.274037757262;TFAP2{A,C}:0.253880294874;MYBL2:0.239519181599;IKZF2:0.224478047202;SOX{8,9,10}:0.21810645071;ARID5B:0.186322219504;FOXQ1:0.172422822453;MYB:0.164122792692;HSF1,2:0.156904654978;YY1:0.136395802029;POU6F1:0.127738698027;MAZ:0.120051481975;NFIX:0.109860200097;ADNP_IRX_SIX_ZHX:0.0958028586955;DBP:0.0952652606431;ZIC1..3:0.0891860578316;ZBTB6:0.0855387833056;MTF1:0.0805692731945;ZNF423:0.0776473296582;IRF7:0.0679046621002;XBP1:0.0589545011353;ATF4:0.0474919590463;GZF1:0.0460567575404;HOX{A4,D4}:0.0438459328565;FOXA2:0.0211721089669;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.00748304116042;STAT2,4,6:0.00187998783473;HNF4A_NR2F1,2:-0.000436405410227;FOXL1:-0.0117198810429;BACH2:-0.0157863368341;NFE2:-0.0231095215719;TEAD1:-0.031878454722;AHR_ARNT_ARNT2:-0.0367582272544;ONECUT1,2:-0.0441563402412;HLF:-0.050388949405;MZF1:-0.0529859593672;NFATC1..3:-0.0566699800749;CUX2:-0.0568091727962;PITX1..3:-0.0710730235992;GATA4:-0.0868464763941;SOX5:-0.0870796042102;TOPORS:-0.08801019065;ELF1,2,4:-0.0955671413874;IKZF1:-0.101373215083;RREB1:-0.106269229796;HNF1A:-0.125065165048;GTF2I:-0.134665990832;UFEwm:-0.140156267138;TFCP2:-0.140496693019;NR3C1:-0.144304562769;FOX{F1,F2,J1}:-0.147102934059;FOXD3:-0.157141815639;LEF1_TCF7_TCF7L1,2:-0.157241127327;SOX2:-0.160909033548;GCM1,2:-0.181586127885;TBP:-0.184294151966;NFKB1_REL_RELA:-0.18980170017;EBF1:-0.194236593888;NR5A1,2:-0.218791412532;NKX6-1,2:-0.239555456677;OCT4_SOX2{dimer}:-0.244917326938;FOXP1:-0.245291676217;POU5F1:-0.253020059293;REST:-0.253052000366;FOS_FOS{B,L1}_JUN{B,D}:-0.261117738304;POU1F1:-0.27756920459;FOXO1,3,4:-0.279823137873;PRDM1:-0.281127303905;PAX3,7:-0.28142724543;SRF:-0.28157236105;FOXM1:-0.285457391837;ZNF148:-0.292089375065;GATA6:-0.305878557243;ETS1,2:-0.306470603347;HIF1A:-0.312125836891;NFE2L2:-0.338423874367;NFIL3:-0.340215864662;GFI1B:-0.347824737322;ESR1:-0.347844824044;LHX3,4:-0.350542757068;TP53:-0.356904574262;CEBPA,B_DDIT3:-0.360259121875;MEF2{A,B,C,D}:-0.364999582967;BPTF:-0.36996580869;SPIB:-0.37046862817;CRX:-0.380609834112;PDX1:-0.385244141935;RUNX1..3:-0.385463679156;EVI1:-0.394401029622;FOSL2:-0.427094983647;ATF5_CREB3:-0.435685498644;SPI1:-0.443026766121;CREB1:-0.444401533698;AIRE:-0.446851545501;MYFfamily:-0.451124942194;POU2F1..3:-0.462163126373;STAT5{A,B}:-0.467491795805;NR6A1:-0.47312808096;ALX4:-0.482632564861;NKX3-1:-0.493402937392;NANOG:-0.501339632044;PAX4:-0.501574822573;RXRA_VDR{dimer}:-0.519838769736;HAND1,2:-0.541052250631;HMGA1,2:-0.541338811395;GLI1..3:-0.541744049144;T:-0.542989362266;RFX2..5_RFXANK_RFXAP:-0.544678700095;MYOD1:-0.553089032147;ZBTB16:-0.556313988148;TFAP4:-0.55778940209;NKX2-1,4:-0.566630180937;SNAI1..3:-0.580509012366;NHLH1,2:-0.585093688838;KLF4:-0.585446038529;NFE2L1:-0.591171574908;SREBF1,2:-0.600098595435;AR:-0.602034593511;ESRRA:-0.619809893707;TBX4,5:-0.623860209351;DMAP1_NCOR{1,2}_SMARC:-0.642959637263;ATF6:-0.653581454722;JUN:-0.653954314855;TLX2:-0.67467265102;FOXP3:-0.681367292113;FOXN1:-0.699889608453;ALX1:-0.70160223848;TGIF1:-0.709687109222;ZEB1:-0.715315080574;LMO2:-0.78426734482;HBP1_HMGB_SSRP1_UBTF:-0.819694195982;POU3F1..4:-0.845602447167;ZNF238:-0.846316039506;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.849270262662;TAL1_TCF{3,4,12}:-0.859959658006;HOXA9_MEIS1:-0.863412365611;NANOG{mouse}:-0.898830968139;VSX1,2:-0.935646433504;ATF2:-0.957023674605;ZNF384:-0.960571823661;SPZ1:-0.984276711525;PAX2:-1.03096608193;SMAD1..7,9:-1.07553596676;NKX2-2,8:-1.09872098322;HMX1:-1.11057608874;EP300:-1.19024890231;NKX3-2:-1.20925738753;NR1H4:-1.27985677035;MAFB:-1.54522531583 | |||
}} | }} |
Revision as of 14:13, 21 March 2012
Name: | liposarcoma cell line:SW 872 |
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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: CNhs11851
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: CNhs11851
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: CNhs11851
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
FF:0103743 SW-872 cell 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
DOID: Disease
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
4 (disease)
UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)
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