FF:12179-129A1: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000178,UBERON:0000179,UBERON:0000463,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0001009,UBERON:0001062,UBERON:0002193,UBERON:0002390,UBERON:0004535,UBERON:0007023 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
| | |comment= | ||
|created_by= | |||
|creation_date= | |||
|def= | |||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
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|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|id=FF:12179-129A1 | |||
|is_a=EFO:0002091;;FF:0000002;;FF:0000210;;FF:0000281 | |is_a=EFO:0002091;;FF:0000002;;FF:0000210;;FF:0000281 | ||
|name=Whole blood (ribopure), donor090309, donation1 | |||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan=,,, | |||
|profile_hcage=CNhs11675,LSID808,release008,COMPLETED | |||
|profile_rnaseq=RDhi10000,,, | |||
|profile_srnaseq=,,, | |||
|rna_box=129 | |||
|rna_catalog_number= | |||
|rna_concentration=0.431 | |||
|rna_extraction_protocol= | |||
|rna_lot_number= | |||
|rna_od260/230=2.06 | |||
|rna_od260/280=1.96 | |||
|rna_position=A1 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=129A1 | |||
|rna_weight_ug=5.2 | |||
|sample_age= | |||
|sample_cell_catalog= | |||
|sample_cell_line= | |||
|sample_cell_lot=090309-02 | |||
|sample_cell_type=CELL MIXTURE - tissue sample | |||
|sample_collaboration=Matched_genome_OSC(contact:Al Forrest) | |||
|sample_company= | |||
|sample_description= | |||
|sample_dev_stage= | |||
|sample_disease= | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity= | |||
|sample_experimental_condition= | |||
|sample_id=12179 | |||
|sample_note= | |||
|sample_sex= | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=blood | |||
|top_motifs=GATA6:4.20543272298;ETS1,2:2.49966190304;SPI1:2.39286413303;SPIB:2.3460863717;ELF1,2,4:2.3290932897;FOXO1,3,4:2.15317458973;NANOG{mouse}:2.07887539572;T:2.03156172799;RUNX1..3:2.00524380578;FOXD3:1.98139227345;FOX{D1,D2}:1.88966458868;DMAP1_NCOR{1,2}_SMARC:1.79881857898;FOXP3:1.68664566568;TLX2:1.63088489865;FOX{F1,F2,J1}:1.58851372852;SPZ1:1.58299606607;STAT5{A,B}:1.4268013472;IRF7:1.40310251564;STAT1,3:1.34478428014;CEBPA,B_DDIT3:1.30346838132;ZNF148:1.25476473459;IRF1,2:1.11624146203;PAX3,7:1.09027965;PAX2:1.08083733554;TFAP4:1.07415046324;TGIF1:1.05845323794;EP300:1.00072596375;FOXN1:0.996717209766;STAT2,4,6:0.936162037659;HMX1:0.890594385202;RXRA_VDR{dimer}:0.853792038974;POU5F1:0.801682200415;FOX{I1,J2}:0.79479946596;POU2F1..3:0.730666895484;SMAD1..7,9:0.70171510068;PDX1:0.660999780983;IKZF2:0.660019510277;NFIX:0.650269383101;TFCP2:0.622749130761;NFATC1..3:0.618465627182;MYOD1:0.596914756869;NFE2L2:0.57187386358;FOXA2:0.565507950529;SREBF1,2:0.529940339357;NKX3-2:0.528160348758;MYFfamily:0.481123245062;NR1H4:0.469789747113;CDX1,2,4:0.450778769767;RFX2..5_RFXANK_RFXAP:0.41493197828;RBPJ:0.395958188343;ZNF423:0.383120642532;ZEB1:0.379554858702;NKX2-2,8:0.367883838197;RREB1:0.334703586046;NFIL3:0.321082386238;ATF5_CREB3:0.281263951434;ZNF238:0.258714300331;CRX:0.257326644057;ALX1:0.255775977009;MYB:0.251691641234;HBP1_HMGB_SSRP1_UBTF:0.227180516158;TOPORS:0.224859288676;MAZ:0.21116844939;HLF:0.206583558206;MZF1:0.183862574288;PPARG:0.166955680183;CUX2:0.154393993749;EVI1:0.14982814796;NFE2L1:0.145520126327;NFKB1_REL_RELA:0.121889260462;SNAI1..3:0.0918896797872;DBP:0.0640179160343;TAL1_TCF{3,4,12}:0.0607260992653;GATA4:0.0522574330687;NFE2:0.051221580275;BPTF:0.0399317053532;BREu{core}:0.0246247781541;LMO2:0.00259817871074;NKX3-1:-0.00815209023931;SRF:-0.022138435143;CREB1:-0.156681720341;XCPE1{core}:-0.19458065194;SP1:-0.199823027826;OCT4_SOX2{dimer}:-0.252044971947;GLI1..3:-0.271889886513;ELK1,4_GABP{A,B1}:-0.290993426519;RORA:-0.367434145004;AIRE:-0.378574400158;REST:-0.397188224137;ATF2:-0.40331534945;BACH2:-0.429155957581;POU1F1:-0.434785459468;KLF4:-0.444941626349;NR6A1:-0.45112124262;FOSL2:-0.466027493549;LEF1_TCF7_TCF7L1,2:-0.474828010985;ADNP_IRX_SIX_ZHX:-0.501610253892;PRDM1:-0.524321543929;ALX4:-0.526867332509;FOXP1:-0.538632863987;NHLH1,2:-0.552177051943;RFX1:-0.552794588628;PATZ1:-0.563540520522;TBX4,5:-0.58524976347;HIF1A:-0.606790121058;ZFP161:-0.60949432679;NR5A1,2:-0.613302111674;NKX2-1,4:-0.615457679952;ESR1:-0.61621362581;ATF4:-0.634162534144;MTE{core}:-0.640633462821;HMGA1,2:-0.662270171222;PRRX1,2:-0.667884289286;MAFB:-0.669008151875;FOS_FOS{B,L1}_JUN{B,D}:-0.674627346755;NR3C1:-0.675070864261;MEF2{A,B,C,D}:-0.69921139241;HNF4A_NR2F1,2:-0.708128351617;GTF2I:-0.72855156502;HOXA9_MEIS1:-0.739541768574;ZNF143:-0.744329727862;AR:-0.750277652942;JUN:-0.764445451451;NRF1:-0.767069813223;HNF1A:-0.788404042611;MTF1:-0.806160735051;TLX1..3_NFIC{dimer}:-0.807964878726;GCM1,2:-0.845721466856;NFY{A,B,C}:-0.8496969848;YY1:-0.859835269009;XBP1:-0.907281864773;SOX2:-0.91539355389;HIC1:-0.928444167161;TFAP2B:-0.931741424613;ARID5B:-0.943111902577;FOXQ1:-0.954901891478;EGR1..3:-0.957673328706;EN1,2:-0.959980441753;ZBTB16:-0.962942071864;PBX1:-0.966629652029;TFAP2{A,C}:-0.970473189652;PAX5:-0.973426752617;TBP:-0.991830672513;NKX6-1,2:-1.02626510605;MED-1{core}:-1.0457392823;PAX6:-1.04711237438;RXR{A,B,G}:-1.06376789977;PITX1..3:-1.08490517988;NKX2-3_NKX2-5:-1.09821258743;E2F1..5:-1.17724581771;POU6F1:-1.20186720142;EBF1:-1.22701576227;NANOG:-1.23718586438;HES1:-1.24190591592;SOX{8,9,10}:-1.25281838251;VSX1,2:-1.29591918577;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.29616990421;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.2996099046;MYBL2:-1.30235895254;GZF1:-1.32555586701;TP53:-1.34784928939;ZBTB6:-1.35495840394;GFI1:-1.35711692315;PAX4:-1.37051181095;UFEwm:-1.37350188532;AHR_ARNT_ARNT2:-1.38814729929;SOX5:-1.39096089032;LHX3,4:-1.4003741195;HAND1,2:-1.46573890415;FOXL1:-1.56511507205;FOXM1:-1.62844783121;GFI1B:-1.62872407897;POU3F1..4:-1.63000470793;ZNF384:-1.63416704945;bHLH_family:-1.66820134364;TEAD1:-1.6936194536;PAX1,9:-1.74042500615;HSF1,2:-1.78247307525;PAX8:-1.81547346415;ATF6:-1.82771463283;ONECUT1,2:-1.85555539974;HOX{A5,B5}:-1.89440459227;HOX{A6,A7,B6,B7}:-1.93401594619;ESRRA:-1.96968137692;ZIC1..3:-1.96989058151;GTF2A1,2:-1.97476705869;TFDP1:-2.09033274234;SOX17:-2.09213753715;HOX{A4,D4}:-2.33493553979;TEF:-2.60428047899;CDC5L:-2.61308799761;IKZF1:-2.85582762568 | |||
}} | }} |
Revision as of 15:06, 21 March 2012
Name: | Whole blood (ribopure), donor090309, donation1 |
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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: CNhs11675
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: CNhs11675
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: CNhs11675
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000002 in vivo cell sample
FF:0000210 human sample
FF:0000281 human whole blood 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
UBERON: Anatomy
0000061 (anatomical structure)
0000178 (blood)
0000179 (haemolymphatic fluid)
0000463 (organism substance)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0002193 (hemolymphoid system)
0002390 (hematopoietic system)
0004535 (cardiovascular system)
0007023 (adult organism)
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