Personal tools

FF:10016-101C7: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:10016-101C7
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0001009,UBERON:0001062,UBERON:0007023,UBERON:0007100
|name=heart, adult, pool1
|sample_id=10016
|rna_tube_id=101C7
|rna_box=101
|rna_position=C7
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Ambion
|rna_lot_number=0910061 -7
|rna_catalog_number=Cat:AM6000 Lot:0910061 -7
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=70,73,74 years old adult
|sample_tissue=heart
|sample_donor(cell lot)=3 pool
|sample_sex=mixed
|sample_age=
|sample_ethnicity=C
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=normal
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-ToTALLY-RNA-v1.0
|rna_weight_ug=10
|rna_concentration=1
|sample_note=
|profile_hcage=CNhs10621,LSID656,release008,COMPLETED
|profile_cagescan=NCig10015,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0001009,UBERON:0001062,UBERON:0007023,UBERON:0007100
|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 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=MEF2{A,B,C,D}:6.48104991213;NR5A1,2:4.50060125315;ESRRA:3.7861637229;AR:3.09341120984;NR1H4:3.0901480566;NFE2L1:2.44193565651;TGIF1:2.33423214712;SRF:2.32291209181;NKX2-2,8:2.16710790292;TFAP4:2.11187898803;RBPJ:2.1034963571;HOX{A4,D4}:2.07528532421;FOXL1:2.07490775847;MAFB:2.00447924754;GCM1,2:1.95890322245;NFATC1..3:1.890851355;PAX6:1.88886663844;TFAP2{A,C}:1.86417432518;GATA6:1.69346600116;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.63370097207;NHLH1,2:1.59971472265;TFCP2:1.59797951989;TLX1..3_NFIC{dimer}:1.51067775654;EP300:1.50797503423;NFIX:1.47652986674;SOX5:1.45293883019;HAND1,2:1.44598832254;RXR{A,B,G}:1.43075573158;RORA:1.35545239256;NANOG:1.33801556159;MTF1:1.3345504017;IKZF1:1.32656345573;SMAD1..7,9:1.31412918718;PATZ1:1.26575480244;TFAP2B:1.25597301289;MYOD1:1.25170540291;HIC1:1.24006696621;MAZ:1.23868814968;MYBL2:1.18399028607;SP1:1.18380919411;NR6A1:1.17089584944;GTF2A1,2:1.13577135042;GFI1B:1.13414066784;PAX1,9:1.11209297504;CUX2:1.09324882181;TBP:1.09114256703;FOX{D1,D2}:1.04918186383;TEAD1:1.03846891985;FOXO1,3,4:1.00243005451;PDX1:0.964438073272;EGR1..3:0.923615444967;MTE{core}:0.866083705897;SPZ1:0.843622676977;MED-1{core}:0.808605558775;ZNF238:0.795215221342;GATA4:0.69615027593;TBX4,5:0.686665854328;STAT2,4,6:0.670782955932;XBP1:0.668841715952;POU3F1..4:0.655223739298;ZNF148:0.653273640836;PPARG:0.653197976797;ZFP161:0.637569072857;NR3C1:0.624070924236;NKX6-1,2:0.613929850605;MZF1:0.607140775009;EN1,2:0.567052094274;IKZF2:0.551721398476;BREu{core}:0.54873523896;JUN:0.521281205386;FOXA2:0.518905593589;GTF2I:0.469315771104;ZNF423:0.460921184793;TLX2:0.447192972476;HSF1,2:0.41136260222;ATF2:0.406172630717;CDC5L:0.403670607903;HOX{A6,A7,B6,B7}:0.396129115702;MYFfamily:0.38987589331;XCPE1{core}:0.367669946431;ZIC1..3:0.335754291512;REST:0.331724365391;RREB1:0.314346607213;SREBF1,2:0.303333776762;FOXP3:0.28041122887;PBX1:0.251406875741;FOXQ1:0.224108646033;FOX{F1,F2,J1}:0.223743543772;FOSL2:0.222379526304;POU6F1:0.222228674661;RFX2..5_RFXANK_RFXAP:0.21423178568;IRF7:0.20068594342;CDX1,2,4:0.197662666321;EVI1:0.192432921551;HNF4A_NR2F1,2:0.189693439635;STAT1,3:0.130492578128;LMO2:0.123065651295;ATF4:0.118737505074;GLI1..3:0.0980045436276;SOX{8,9,10}:0.0861209012243;ETS1,2:0.0744106868348;LEF1_TCF7_TCF7L1,2:0.0442175022383;T:0.0283125481031;BPTF:0.023964618576;ADNP_IRX_SIX_ZHX:0.0184847434279;ESR1:0.0154295116691;KLF4:-0.00644843905123;ATF6:-0.0312601207057;NKX3-1:-0.0567427909584;HNF1A:-0.0631014587057;RXRA_VDR{dimer}:-0.0648949717824;UFEwm:-0.0874020246048;ATF5_CREB3:-0.102264496986;STAT5{A,B}:-0.11551629302;HMX1:-0.119279021788;PAX5:-0.125550604926;ZEB1:-0.128232353595;PRDM1:-0.156672635026;SPI1:-0.157070584346;SOX17:-0.165104481609;CEBPA,B_DDIT3:-0.174504171053;FOXP1:-0.189125084625;VSX1,2:-0.193542425434;HLF:-0.198791889123;FOXN1:-0.222045508181;EBF1:-0.25677839711;SNAI1..3:-0.260093427134;NFE2:-0.260194590202;CREB1:-0.269808553833;NFE2L2:-0.271089463153;ZNF143:-0.271501576459;NKX3-2:-0.272949431933;DMAP1_NCOR{1,2}_SMARC:-0.287332159236;HOX{A5,B5}:-0.296070466213;GZF1:-0.301545914866;SPIB:-0.302206387048;TP53:-0.311689980598;NFIL3:-0.312090108484;IRF1,2:-0.321172581567;NANOG{mouse}:-0.324997272731;PRRX1,2:-0.386093153042;POU1F1:-0.414620004087;YY1:-0.439038437023;GFI1:-0.441931765321;TFDP1:-0.444603826429;HOXA9_MEIS1:-0.463007245439;PAX2:-0.475141555534;NRF1:-0.491376564718;LHX3,4:-0.494361474039;HMGA1,2:-0.504193299474;FOS_FOS{B,L1}_JUN{B,D}:-0.524762630263;ARID5B:-0.530972048435;CRX:-0.557353297497;NFKB1_REL_RELA:-0.576590827657;HBP1_HMGB_SSRP1_UBTF:-0.591041208401;BACH2:-0.602340694284;TEF:-0.631414388387;ONECUT1,2:-0.650593266864;NFY{A,B,C}:-0.65825362267;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.678976717226;NKX2-1,4:-0.688138337516;FOX{I1,J2}:-0.693189763684;ELF1,2,4:-0.722626960766;bHLH_family:-0.737239295454;FOXD3:-0.737974545443;TAL1_TCF{3,4,12}:-0.742631969226;RUNX1..3:-0.794354807945;RFX1:-0.837257526407;ALX1:-0.889210825302;ALX4:-0.928979637147;ZBTB16:-0.991541089069;OCT4_SOX2{dimer}:-1.01713842288;PAX3,7:-1.0378988459;PITX1..3:-1.04378675697;SOX2:-1.04494021476;E2F1..5:-1.06433275676;ZBTB6:-1.10180572821;POU5F1:-1.10261016005;HES1:-1.13324985944;DBP:-1.14836301675;FOXM1:-1.1841344357;MYB:-1.39904408986;NKX2-3_NKX2-5:-1.40138957064;AHR_ARNT_ARNT2:-1.47939142349;TOPORS:-1.48637478613;ELK1,4_GABP{A,B1}:-1.52274052288;POU2F1..3:-1.52616413843;PAX4:-1.57139302949;HIF1A:-1.67361915661;ZNF384:-1.75387175802;AIRE:-2.21174488336;PAX8:-2.30981404458
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10016-101C7
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010016
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010016
|name=heart, adult, pool1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=NCig10015,,,
|profile_hcage=CNhs10621,LSID656,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=101
|rna_catalog_number=Cat:AM6000 Lot:0910061 -7
|rna_concentration=1
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-ToTALLY-RNA-v1.0
|rna_lot_number=0910061 -7
|rna_od260/230=
|rna_od260/280=
|rna_position=C7
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=101C7
|rna_weight_ug=10
|sample_age=
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=NA
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Ambion
|sample_description=
|sample_dev_stage=70,73,74 years old adult
|sample_disease=normal
|sample_donor(cell lot)=3 pool
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=10016
|sample_note=
|sample_sex=mixed
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=heart
|top_motifs=MEF2{A,B,C,D}:6.48104991213;NR5A1,2:4.50060125315;ESRRA:3.7861637229;AR:3.09341120984;NR1H4:3.0901480566;NFE2L1:2.44193565651;TGIF1:2.33423214712;SRF:2.32291209181;NKX2-2,8:2.16710790292;TFAP4:2.11187898803;RBPJ:2.1034963571;HOX{A4,D4}:2.07528532421;FOXL1:2.07490775847;MAFB:2.00447924754;GCM1,2:1.95890322245;NFATC1..3:1.890851355;PAX6:1.88886663844;TFAP2{A,C}:1.86417432518;GATA6:1.69346600116;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.63370097207;NHLH1,2:1.59971472265;TFCP2:1.59797951989;TLX1..3_NFIC{dimer}:1.51067775654;EP300:1.50797503423;NFIX:1.47652986674;SOX5:1.45293883019;HAND1,2:1.44598832254;RXR{A,B,G}:1.43075573158;RORA:1.35545239256;NANOG:1.33801556159;MTF1:1.3345504017;IKZF1:1.32656345573;SMAD1..7,9:1.31412918718;PATZ1:1.26575480244;TFAP2B:1.25597301289;MYOD1:1.25170540291;HIC1:1.24006696621;MAZ:1.23868814968;MYBL2:1.18399028607;SP1:1.18380919411;NR6A1:1.17089584944;GTF2A1,2:1.13577135042;GFI1B:1.13414066784;PAX1,9:1.11209297504;CUX2:1.09324882181;TBP:1.09114256703;FOX{D1,D2}:1.04918186383;TEAD1:1.03846891985;FOXO1,3,4:1.00243005451;PDX1:0.964438073272;EGR1..3:0.923615444967;MTE{core}:0.866083705897;SPZ1:0.843622676977;MED-1{core}:0.808605558775;ZNF238:0.795215221342;GATA4:0.69615027593;TBX4,5:0.686665854328;STAT2,4,6:0.670782955932;XBP1:0.668841715952;POU3F1..4:0.655223739298;ZNF148:0.653273640836;PPARG:0.653197976797;ZFP161:0.637569072857;NR3C1:0.624070924236;NKX6-1,2:0.613929850605;MZF1:0.607140775009;EN1,2:0.567052094274;IKZF2:0.551721398476;BREu{core}:0.54873523896;JUN:0.521281205386;FOXA2:0.518905593589;GTF2I:0.469315771104;ZNF423:0.460921184793;TLX2:0.447192972476;HSF1,2:0.41136260222;ATF2:0.406172630717;CDC5L:0.403670607903;HOX{A6,A7,B6,B7}:0.396129115702;MYFfamily:0.38987589331;XCPE1{core}:0.367669946431;ZIC1..3:0.335754291512;REST:0.331724365391;RREB1:0.314346607213;SREBF1,2:0.303333776762;FOXP3:0.28041122887;PBX1:0.251406875741;FOXQ1:0.224108646033;FOX{F1,F2,J1}:0.223743543772;FOSL2:0.222379526304;POU6F1:0.222228674661;RFX2..5_RFXANK_RFXAP:0.21423178568;IRF7:0.20068594342;CDX1,2,4:0.197662666321;EVI1:0.192432921551;HNF4A_NR2F1,2:0.189693439635;STAT1,3:0.130492578128;LMO2:0.123065651295;ATF4:0.118737505074;GLI1..3:0.0980045436276;SOX{8,9,10}:0.0861209012243;ETS1,2:0.0744106868348;LEF1_TCF7_TCF7L1,2:0.0442175022383;T:0.0283125481031;BPTF:0.023964618576;ADNP_IRX_SIX_ZHX:0.0184847434279;ESR1:0.0154295116691;KLF4:-0.00644843905123;ATF6:-0.0312601207057;NKX3-1:-0.0567427909584;HNF1A:-0.0631014587057;RXRA_VDR{dimer}:-0.0648949717824;UFEwm:-0.0874020246048;ATF5_CREB3:-0.102264496986;STAT5{A,B}:-0.11551629302;HMX1:-0.119279021788;PAX5:-0.125550604926;ZEB1:-0.128232353595;PRDM1:-0.156672635026;SPI1:-0.157070584346;SOX17:-0.165104481609;CEBPA,B_DDIT3:-0.174504171053;FOXP1:-0.189125084625;VSX1,2:-0.193542425434;HLF:-0.198791889123;FOXN1:-0.222045508181;EBF1:-0.25677839711;SNAI1..3:-0.260093427134;NFE2:-0.260194590202;CREB1:-0.269808553833;NFE2L2:-0.271089463153;ZNF143:-0.271501576459;NKX3-2:-0.272949431933;DMAP1_NCOR{1,2}_SMARC:-0.287332159236;HOX{A5,B5}:-0.296070466213;GZF1:-0.301545914866;SPIB:-0.302206387048;TP53:-0.311689980598;NFIL3:-0.312090108484;IRF1,2:-0.321172581567;NANOG{mouse}:-0.324997272731;PRRX1,2:-0.386093153042;POU1F1:-0.414620004087;YY1:-0.439038437023;GFI1:-0.441931765321;TFDP1:-0.444603826429;HOXA9_MEIS1:-0.463007245439;PAX2:-0.475141555534;NRF1:-0.491376564718;LHX3,4:-0.494361474039;HMGA1,2:-0.504193299474;FOS_FOS{B,L1}_JUN{B,D}:-0.524762630263;ARID5B:-0.530972048435;CRX:-0.557353297497;NFKB1_REL_RELA:-0.576590827657;HBP1_HMGB_SSRP1_UBTF:-0.591041208401;BACH2:-0.602340694284;TEF:-0.631414388387;ONECUT1,2:-0.650593266864;NFY{A,B,C}:-0.65825362267;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.678976717226;NKX2-1,4:-0.688138337516;FOX{I1,J2}:-0.693189763684;ELF1,2,4:-0.722626960766;bHLH_family:-0.737239295454;FOXD3:-0.737974545443;TAL1_TCF{3,4,12}:-0.742631969226;RUNX1..3:-0.794354807945;RFX1:-0.837257526407;ALX1:-0.889210825302;ALX4:-0.928979637147;ZBTB16:-0.991541089069;OCT4_SOX2{dimer}:-1.01713842288;PAX3,7:-1.0378988459;PITX1..3:-1.04378675697;SOX2:-1.04494021476;E2F1..5:-1.06433275676;ZBTB6:-1.10180572821;POU5F1:-1.10261016005;HES1:-1.13324985944;DBP:-1.14836301675;FOXM1:-1.1841344357;MYB:-1.39904408986;NKX2-3_NKX2-5:-1.40138957064;AHR_ARNT_ARNT2:-1.47939142349;TOPORS:-1.48637478613;ELK1,4_GABP{A,B1}:-1.52274052288;POU2F1..3:-1.52616413843;PAX4:-1.57139302949;HIF1A:-1.67361915661;ZNF384:-1.75387175802;AIRE:-2.21174488336;PAX8:-2.30981404458
}}
}}

Revision as of 14:00, 21 March 2012


Name:heart, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueheart
dev stage70,73,74 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -7
catalog numberCat:AM6000 Lot:0910061 -7
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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

library id: CNhs10621



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: CNhs10621



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: CNhs10621


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
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0007023 (adult organism)
0007100 (primary circulatory organ)

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