Personal tools

FF:10170-103B8: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:10170-103B8
|ancestors_in_anatomy_facet=
|name=medial frontal gyrus - adult, donor10196
|sample_id=10170
|rna_tube_id=103B8
|rna_box=103
|rna_position=B8
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=medial frontal gyrus
|sample_donor(cell lot)=donor: 10196
|sample_sex=female
|sample_age=60
|sample_ethnicity=
|rna_rin=
|rna_od260/230=2.24
|rna_od260/280=2.08
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=Peter Heutink
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=73.872
|rna_concentration=0.98496
|sample_note=
|profile_hcage=CNhs13796,LSID1086,release014,COMPLETED
|profile_cagescan=
|profile_srnaseq=
|profile_rnaseq=
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=
|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=REST:3.84545321499;DBP:3.81859156824;CUX2:3.7793412588;AHR_ARNT_ARNT2:3.56084025405;HOXA9_MEIS1:3.54329798001;ALX1:3.47064498332;FOXM1:3.42476012412;PRRX1,2:3.41505757918;MYFfamily:3.37601402099;NHLH1,2:3.31138488845;PAX4:2.96685078489;ZFP161:2.91108580876;ZBTB6:2.87918538548;PRDM1:2.81199649804;EGR1..3:2.79386506918;MTE{core}:2.77682656593;OCT4_SOX2{dimer}:2.75925709074;MED-1{core}:2.73950315323;MTF1:2.66162560826;RFX1:2.55906497362;ATF2:2.55595144715;NKX3-2:2.54836695308;PAX6:2.53704882334;ARID5B:2.51711921939;RREB1:2.47201295929;GATA4:2.40756016503;POU6F1:2.31533650987;JUN:2.23943651892;PAX5:2.10157755318;HOX{A4,D4}:2.05819196466;FOXQ1:2.02203921703;GTF2I:2.00232274179;POU1F1:1.9684342728;CDC5L:1.95181322628;POU5F1:1.92773051636;NKX2-3_NKX2-5:1.91480106264;MZF1:1.91064058507;KLF4:1.88292160786;POU3F1..4:1.77943793677;GFI1B:1.77924096884;NRF1:1.77844219955;BREu{core}:1.77318314822;RFX2..5_RFXANK_RFXAP:1.74933402428;TFAP2B:1.65569267537;TGIF1:1.62943810273;SOX17:1.61910026113;ESRRA:1.56640416679;HMGA1,2:1.54531047588;LEF1_TCF7_TCF7L1,2:1.53733454483;LMO2:1.53420316849;HBP1_HMGB_SSRP1_UBTF:1.53204223241;HIC1:1.5086737026;TFDP1:1.43117052173;ZNF384:1.40286977326;SOX{8,9,10}:1.39623667033;MAFB:1.38821003157;TEF:1.37883248782;SMAD1..7,9:1.35348444031;CRX:1.32502316108;SOX2:1.32230612668;HAND1,2:1.32008766359;SOX5:1.27914852739;MYOD1:1.27234317115;FOXL1:1.26853666982;PAX1,9:1.2281567727;MAZ:1.20697469555;NKX6-1,2:1.15859569857;IKZF2:1.1259012892;PATZ1:1.11023965359;NFIX:1.10932561014;RORA:1.08364480208;NFIL3:1.06061655733;FOXP1:1.02728617641;FOXD3:1.00685923878;PAX8:0.976406359485;NANOG:0.968329373062;XBP1:0.967803163;ZBTB16:0.966752879678;NR3C1:0.961172773526;ONECUT1,2:0.961013597722;CREB1:0.933086552606;BPTF:0.87548368837;FOX{F1,F2,J1}:0.864286670912;STAT1,3:0.823253320646;FOXP3:0.78581082845;ZEB1:0.768194374982;RBPJ:0.708032815631;ZNF143:0.694453936457;YY1:0.691282438175;TLX2:0.661287428503;GCM1,2:0.608062915781;MEF2{A,B,C,D}:0.527200387978;ADNP_IRX_SIX_ZHX:0.501372578105;SREBF1,2:0.485830846445;ATF4:0.464533597342;ATF5_CREB3:0.452762887444;UFEwm:0.422647277164;EP300:0.351704735503;LHX3,4:0.341818360415;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.315491433711;PAX2:0.312710492346;EBF1:0.29316701014;HMX1:0.277215038224;GTF2A1,2:0.269257843915;IKZF1:0.263377663706;FOXN1:0.259902621237;GZF1:0.25598061686;GFI1:0.19915444842;ZIC1..3:0.182415381778;SPZ1:0.17762783964;TBX4,5:0.141384405882;ZNF238:0.105067249802;MYBL2:0.100170981369;FOX{D1,D2}:0.0785252493351;STAT2,4,6:0.0752305379739;AIRE:0.0643146015505;NFE2L1:0.0475261891059;EVI1:0.0135770632246;DMAP1_NCOR{1,2}_SMARC:0.00287150372035;AR:-0.00192741261789;TLX1..3_NFIC{dimer}:-0.0175547144445;IRF7:-0.0366585780576;NFE2L2:-0.0480377992673;PAX3,7:-0.0856404215727;SNAI1..3:-0.0947105875377;TOPORS:-0.114644505705;HOX{A6,A7,B6,B7}:-0.148258854638;ATF6:-0.16633624285;ZNF423:-0.171732411416;HSF1,2:-0.185885014837;PBX1:-0.232913737003;NFATC1..3:-0.304983624585;VSX1,2:-0.312079182473;NFY{A,B,C}:-0.316574364719;bHLH_family:-0.32433315914;NKX3-1:-0.329796389177;T:-0.343737233847;FOX{I1,J2}:-0.345739623996;SP1:-0.353072188934;CEBPA,B_DDIT3:-0.377699563458;NANOG{mouse}:-0.391333361959;PDX1:-0.406053955207;NFE2:-0.438755820768;GATA6:-0.453354851201;FOXA2:-0.476754150901;TFAP2{A,C}:-0.515823143766;SPI1:-0.537605526273;CDX1,2,4:-0.58342433059;IRF1,2:-0.646455645698;NR1H4:-0.710342109168;HNF1A:-0.784389347862;SPIB:-0.839064122796;HIF1A:-0.85806873001;FOSL2:-0.885427508033;BACH2:-0.898708493532;FOXO1,3,4:-0.962967957427;NR5A1,2:-0.991070309108;FOS_FOS{B,L1}_JUN{B,D}:-0.995841676502;RXRA_VDR{dimer}:-1.10365356633;ETS1,2:-1.10903787911;HNF4A_NR2F1,2:-1.11722433201;XCPE1{core}:-1.13116983307;RXR{A,B,G}:-1.1544164509;TP53:-1.16874206194;TEAD1:-1.17398713528;RUNX1..3:-1.21156580222;TAL1_TCF{3,4,12}:-1.22680017336;TBP:-1.25666201714;GLI1..3:-1.25843169835;NFKB1_REL_RELA:-1.27259723609;HOX{A5,B5}:-1.3076611939;POU2F1..3:-1.31016558352;E2F1..5:-1.31084729288;NKX2-2,8:-1.33057849262;PITX1..3:-1.34237949017;ELK1,4_GABP{A,B1}:-1.35528336448;HLF:-1.42266887068;MYB:-1.45484172509;ELF1,2,4:-1.47359357078;ZNF148:-1.48354594408;HES1:-1.57287923997;ESR1:-1.59387718262;ALX4:-1.6272846532;TFAP4:-1.64691864737;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.72423113693;PPARG:-1.74167165186;STAT5{A,B}:-1.80621582645;SRF:-1.87193073221;TFCP2:-1.89487464858;NKX2-1,4:-1.9695746773;EN1,2:-2.37037036744;NR6A1:-2.57077146356
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10170-103B8
|is_a=FF:0000004;;FF:0000210;;UBERON:0002702;;UBERON:0007023
|is_a=FF:0000004;;FF:0000210;;UBERON:0002702;;UBERON:0007023
|name=medial frontal gyrus - adult, donor10196
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=
|profile_hcage=CNhs13796,LSID1086,release014,COMPLETED
|profile_rnaseq=
|profile_srnaseq=
|rna_box=103
|rna_catalog_number=
|rna_concentration=0.98496
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.24
|rna_od260/280=2.08
|rna_position=B8
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=103B8
|rna_weight_ug=73.872
|sample_age=60
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=NA
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=Peter Heutink
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=donor: 10196
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10170
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=medial frontal gyrus
|top_motifs=REST:3.84545321499;DBP:3.81859156824;CUX2:3.7793412588;AHR_ARNT_ARNT2:3.56084025405;HOXA9_MEIS1:3.54329798001;ALX1:3.47064498332;FOXM1:3.42476012412;PRRX1,2:3.41505757918;MYFfamily:3.37601402099;NHLH1,2:3.31138488845;PAX4:2.96685078489;ZFP161:2.91108580876;ZBTB6:2.87918538548;PRDM1:2.81199649804;EGR1..3:2.79386506918;MTE{core}:2.77682656593;OCT4_SOX2{dimer}:2.75925709074;MED-1{core}:2.73950315323;MTF1:2.66162560826;RFX1:2.55906497362;ATF2:2.55595144715;NKX3-2:2.54836695308;PAX6:2.53704882334;ARID5B:2.51711921939;RREB1:2.47201295929;GATA4:2.40756016503;POU6F1:2.31533650987;JUN:2.23943651892;PAX5:2.10157755318;HOX{A4,D4}:2.05819196466;FOXQ1:2.02203921703;GTF2I:2.00232274179;POU1F1:1.9684342728;CDC5L:1.95181322628;POU5F1:1.92773051636;NKX2-3_NKX2-5:1.91480106264;MZF1:1.91064058507;KLF4:1.88292160786;POU3F1..4:1.77943793677;GFI1B:1.77924096884;NRF1:1.77844219955;BREu{core}:1.77318314822;RFX2..5_RFXANK_RFXAP:1.74933402428;TFAP2B:1.65569267537;TGIF1:1.62943810273;SOX17:1.61910026113;ESRRA:1.56640416679;HMGA1,2:1.54531047588;LEF1_TCF7_TCF7L1,2:1.53733454483;LMO2:1.53420316849;HBP1_HMGB_SSRP1_UBTF:1.53204223241;HIC1:1.5086737026;TFDP1:1.43117052173;ZNF384:1.40286977326;SOX{8,9,10}:1.39623667033;MAFB:1.38821003157;TEF:1.37883248782;SMAD1..7,9:1.35348444031;CRX:1.32502316108;SOX2:1.32230612668;HAND1,2:1.32008766359;SOX5:1.27914852739;MYOD1:1.27234317115;FOXL1:1.26853666982;PAX1,9:1.2281567727;MAZ:1.20697469555;NKX6-1,2:1.15859569857;IKZF2:1.1259012892;PATZ1:1.11023965359;NFIX:1.10932561014;RORA:1.08364480208;NFIL3:1.06061655733;FOXP1:1.02728617641;FOXD3:1.00685923878;PAX8:0.976406359485;NANOG:0.968329373062;XBP1:0.967803163;ZBTB16:0.966752879678;NR3C1:0.961172773526;ONECUT1,2:0.961013597722;CREB1:0.933086552606;BPTF:0.87548368837;FOX{F1,F2,J1}:0.864286670912;STAT1,3:0.823253320646;FOXP3:0.78581082845;ZEB1:0.768194374982;RBPJ:0.708032815631;ZNF143:0.694453936457;YY1:0.691282438175;TLX2:0.661287428503;GCM1,2:0.608062915781;MEF2{A,B,C,D}:0.527200387978;ADNP_IRX_SIX_ZHX:0.501372578105;SREBF1,2:0.485830846445;ATF4:0.464533597342;ATF5_CREB3:0.452762887444;UFEwm:0.422647277164;EP300:0.351704735503;LHX3,4:0.341818360415;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.315491433711;PAX2:0.312710492346;EBF1:0.29316701014;HMX1:0.277215038224;GTF2A1,2:0.269257843915;IKZF1:0.263377663706;FOXN1:0.259902621237;GZF1:0.25598061686;GFI1:0.19915444842;ZIC1..3:0.182415381778;SPZ1:0.17762783964;TBX4,5:0.141384405882;ZNF238:0.105067249802;MYBL2:0.100170981369;FOX{D1,D2}:0.0785252493351;STAT2,4,6:0.0752305379739;AIRE:0.0643146015505;NFE2L1:0.0475261891059;EVI1:0.0135770632246;DMAP1_NCOR{1,2}_SMARC:0.00287150372035;AR:-0.00192741261789;TLX1..3_NFIC{dimer}:-0.0175547144445;IRF7:-0.0366585780576;NFE2L2:-0.0480377992673;PAX3,7:-0.0856404215727;SNAI1..3:-0.0947105875377;TOPORS:-0.114644505705;HOX{A6,A7,B6,B7}:-0.148258854638;ATF6:-0.16633624285;ZNF423:-0.171732411416;HSF1,2:-0.185885014837;PBX1:-0.232913737003;NFATC1..3:-0.304983624585;VSX1,2:-0.312079182473;NFY{A,B,C}:-0.316574364719;bHLH_family:-0.32433315914;NKX3-1:-0.329796389177;T:-0.343737233847;FOX{I1,J2}:-0.345739623996;SP1:-0.353072188934;CEBPA,B_DDIT3:-0.377699563458;NANOG{mouse}:-0.391333361959;PDX1:-0.406053955207;NFE2:-0.438755820768;GATA6:-0.453354851201;FOXA2:-0.476754150901;TFAP2{A,C}:-0.515823143766;SPI1:-0.537605526273;CDX1,2,4:-0.58342433059;IRF1,2:-0.646455645698;NR1H4:-0.710342109168;HNF1A:-0.784389347862;SPIB:-0.839064122796;HIF1A:-0.85806873001;FOSL2:-0.885427508033;BACH2:-0.898708493532;FOXO1,3,4:-0.962967957427;NR5A1,2:-0.991070309108;FOS_FOS{B,L1}_JUN{B,D}:-0.995841676502;RXRA_VDR{dimer}:-1.10365356633;ETS1,2:-1.10903787911;HNF4A_NR2F1,2:-1.11722433201;XCPE1{core}:-1.13116983307;RXR{A,B,G}:-1.1544164509;TP53:-1.16874206194;TEAD1:-1.17398713528;RUNX1..3:-1.21156580222;TAL1_TCF{3,4,12}:-1.22680017336;TBP:-1.25666201714;GLI1..3:-1.25843169835;NFKB1_REL_RELA:-1.27259723609;HOX{A5,B5}:-1.3076611939;POU2F1..3:-1.31016558352;E2F1..5:-1.31084729288;NKX2-2,8:-1.33057849262;PITX1..3:-1.34237949017;ELK1,4_GABP{A,B1}:-1.35528336448;HLF:-1.42266887068;MYB:-1.45484172509;ELF1,2,4:-1.47359357078;ZNF148:-1.48354594408;HES1:-1.57287923997;ESR1:-1.59387718262;ALX4:-1.6272846532;TFAP4:-1.64691864737;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.72423113693;PPARG:-1.74167165186;STAT5{A,B}:-1.80621582645;SRF:-1.87193073221;TFCP2:-1.89487464858;NKX2-1,4:-1.9695746773;EN1,2:-2.37037036744;NR6A1:-2.57077146356
}}
}}

Revision as of 14:03, 21 March 2012


Name:medial frontal gyrus - adult, donor10196
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemedial frontal gyrus
dev stageNA
sexfemale
age60
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
CollapseHg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
CollapseHg38
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: CNhs13796



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: CNhs13796



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: CNhs13796


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

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