Personal tools

FF:10070-101I7: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:10070-101I7
|ancestors_in_anatomy_facet=UBERON:0000059,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000160,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001155,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0004185,UBERON:0004921,UBERON:0005409,UBERON:0005423,UBERON:0007026
|name=colon, fetal, donor1
|sample_id=10070
|rna_tube_id=101I7
|rna_box=101
|rna_position=I7
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Biochain
|rna_lot_number=B207218
|rna_catalog_number=Cat:RtHFN: Colon
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=37 weeks fetus
|sample_tissue=colon
|sample_donor(cell lot)=1
|sample_sex=female
|sample_age=
|sample_ethnicity=A?
|rna_rin=6.9
|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-TRIzol-isopropanol-v1.0
|rna_weight_ug=50
|rna_concentration=2
|sample_note=
|profile_hcage=CNhs11780,LSID820,release009,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000059,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000160,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001155,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0004185,UBERON:0004921,UBERON:0005409,UBERON:0005423,UBERON:0007026
|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=HNF4A_NR2F1,2:4.23213585725;HNF1A:3.66884520747;FOXD3:2.92721141115;DBP:2.84435762306;MTF1:2.81686810515;T:2.61933567985;FOXL1:2.58024244692;IKZF2:2.15092046023;SRF:2.14168067706;TBP:2.12472495717;MYBL2:2.08668101871;SPZ1:2.0599219404;XCPE1{core}:1.99725479595;SNAI1..3:1.96979491823;SP1:1.90238550067;PRDM1:1.89061090688;MAZ:1.87940120276;TFCP2:1.8553722361;NKX2-3_NKX2-5:1.81415899514;ZEB1:1.78904647683;FOXP1:1.78685258251;MTE{core}:1.74624593916;POU5F1:1.73557120817;FOX{D1,D2}:1.72386018613;HOX{A6,A7,B6,B7}:1.70894389693;FOXO1,3,4:1.66219272129;MZF1:1.5851454858;PATZ1:1.55926687621;BPTF:1.49623422813;NR6A1:1.48900555928;GATA6:1.47894814979;EP300:1.43587610272;NR1H4:1.40816470151;TFAP2{A,C}:1.40513847116;HIC1:1.31105079078;MED-1{core}:1.30463449407;TFAP2B:1.29705018936;POU6F1:1.28187940821;ZNF148:1.22778671672;GTF2I:1.2242285745;PAX6:1.21775999506;GATA4:1.21279719842;FOXM1:1.18084071155;FOX{F1,F2,J1}:1.13621634746;MYFfamily:1.13231817325;ATF6:1.08443081382;CDX1,2,4:0.980958589194;FOX{I1,J2}:0.977353080066;HMX1:0.951260868394;NR3C1:0.915552555352;TFAP4:0.875596755923;SOX5:0.871518726484;HMGA1,2:0.864941462929;EGR1..3:0.853071321553;RREB1:0.830396714929;ADNP_IRX_SIX_ZHX:0.76746501804;TLX1..3_NFIC{dimer}:0.754033857862;ZNF423:0.748703294938;KLF4:0.740733319254;PAX5:0.734497719607;GLI1..3:0.70711404082;ZNF384:0.682187218849;PITX1..3:0.681982415327;RBPJ:0.672149374115;TOPORS:0.664290227836;GCM1,2:0.653494589304;LMO2:0.635429670296;DMAP1_NCOR{1,2}_SMARC:0.619843979697;GFI1B:0.616204720529;FOXA2:0.581385353441;CDC5L:0.572563068833;NKX2-1,4:0.570737997596;REST:0.51365822469;BREu{core}:0.513378687311;NANOG:0.505067084883;ZFP161:0.503443049801;TBX4,5:0.479670834272;ESR1:0.477763227168;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.445436194414;TLX2:0.441731245489;AIRE:0.43723950399;GZF1:0.429957972387;STAT2,4,6:0.42871658779;ETS1,2:0.419707345702;NR5A1,2:0.404890749786;RXR{A,B,G}:0.398015363059;HBP1_HMGB_SSRP1_UBTF:0.38216244883;SMAD1..7,9:0.366898228539;FOXQ1:0.346184291509;NHLH1,2:0.303458841284;NKX6-1,2:0.296673129856;ZBTB16:0.29397817605;MYOD1:0.283713574434;ONECUT1,2:0.274304394335;LEF1_TCF7_TCF7L1,2:0.270652991381;IRF1,2:0.266366385871;PRRX1,2:0.264860811124;SREBF1,2:0.262662889797;FOXN1:0.250024411737;POU1F1:0.244389866355;TEAD1:0.238992918624;IRF7:0.236491033827;GFI1:0.222604034826;VSX1,2:0.208263903414;AR:0.177607199101;NANOG{mouse}:0.175305862636;OCT4_SOX2{dimer}:0.149752044949;GTF2A1,2:0.132352578058;TAL1_TCF{3,4,12}:0.129024875331;ATF2:0.124985083456;SPIB:0.11559387634;ATF4:0.0800809538856;MEF2{A,B,C,D}:0.0421905176269;EBF1:0.0397754858405;NKX2-2,8:0.038648093772;SPI1:0.0336800546134;ESRRA:0.0333479047093;NFATC1..3:-0.00630082737492;ARID5B:-0.00711431547617;ALX1:-0.00923576333128;CUX2:-0.022683158711;UFEwm:-0.0257256273908;STAT1,3:-0.0355782880885;ZBTB6:-0.0363911857766;HES1:-0.0657018756698;FOXP3:-0.0692220927696;SOX2:-0.0957178462632;MAFB:-0.102120632227;POU3F1..4:-0.102933697343;SOX17:-0.120676517407;RXRA_VDR{dimer}:-0.126436122184;POU2F1..3:-0.143264600463;IKZF1:-0.153465641654;CEBPA,B_DDIT3:-0.161090152309;SOX{8,9,10}:-0.182672154111;XBP1:-0.195369062919;RUNX1..3:-0.198735117386;HIF1A:-0.216720428499;ZIC1..3:-0.222411461719;TEF:-0.225369420059;bHLH_family:-0.242763111492;JUN:-0.251132671656;PAX2:-0.255735136584;ZNF238:-0.258133705221;LHX3,4:-0.291154964671;EVI1:-0.309668459;NFKB1_REL_RELA:-0.310313010291;PAX3,7:-0.351176652554;PBX1:-0.393671611483;TGIF1:-0.397953113667;ATF5_CREB3:-0.41646889202;HAND1,2:-0.425530577145;NFIL3:-0.464178212362;ZNF143:-0.478702295528;HLF:-0.479798578914;AHR_ARNT_ARNT2:-0.49893173281;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.50071967433;NFY{A,B,C}:-0.510441157692;FOSL2:-0.527330361871;NFIX:-0.561732019343;NFE2:-0.57686197585;ELF1,2,4:-0.581119500071;PPARG:-0.598214190793;NKX3-2:-0.604446657392;TFDP1:-0.611835991344;TP53:-0.615621654441;E2F1..5:-0.61594453459;CREB1:-0.625413055861;PDX1:-0.643677795292;RFX2..5_RFXANK_RFXAP:-0.676266140636;HOX{A4,D4}:-0.727175040251;FOS_FOS{B,L1}_JUN{B,D}:-0.759227175839;RFX1:-0.80487324359;NKX3-1:-0.844638067187;RORA:-0.844941402991;NRF1:-0.891548501044;CRX:-0.912743834992;NFE2L2:-0.973630430761;BACH2:-0.982125399229;HOX{A5,B5}:-1.07338808665;NFE2L1:-1.12924024331;PAX4:-1.19051072024;ALX4:-1.19693081161;HSF1,2:-1.2863252534;PAX1,9:-1.2864108292;MYB:-1.33801535546;STAT5{A,B}:-1.33862796405;EN1,2:-1.33943718228;HOXA9_MEIS1:-1.50050341398;YY1:-1.6560357995;ELK1,4_GABP{A,B1}:-1.67527325961;PAX8:-2.01552186177
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10070-101I7
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010070
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010070
|name=colon, fetal, donor1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11780,LSID820,release009,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=101
|rna_catalog_number=Cat:RtHFN: Colon
|rna_concentration=2
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=B207218
|rna_od260/230=
|rna_od260/280=
|rna_position=I7
|rna_rin=6.9
|rna_sample_type=total RNA
|rna_tube_id=101I7
|rna_weight_ug=50
|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=Biochain
|sample_description=
|sample_dev_stage=37 weeks fetus
|sample_disease=normal
|sample_donor(cell lot)=1
|sample_ethnicity=A?
|sample_experimental_condition=
|sample_id=10070
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=colon
|top_motifs=HNF4A_NR2F1,2:4.23213585725;HNF1A:3.66884520747;FOXD3:2.92721141115;DBP:2.84435762306;MTF1:2.81686810515;T:2.61933567985;FOXL1:2.58024244692;IKZF2:2.15092046023;SRF:2.14168067706;TBP:2.12472495717;MYBL2:2.08668101871;SPZ1:2.0599219404;XCPE1{core}:1.99725479595;SNAI1..3:1.96979491823;SP1:1.90238550067;PRDM1:1.89061090688;MAZ:1.87940120276;TFCP2:1.8553722361;NKX2-3_NKX2-5:1.81415899514;ZEB1:1.78904647683;FOXP1:1.78685258251;MTE{core}:1.74624593916;POU5F1:1.73557120817;FOX{D1,D2}:1.72386018613;HOX{A6,A7,B6,B7}:1.70894389693;FOXO1,3,4:1.66219272129;MZF1:1.5851454858;PATZ1:1.55926687621;BPTF:1.49623422813;NR6A1:1.48900555928;GATA6:1.47894814979;EP300:1.43587610272;NR1H4:1.40816470151;TFAP2{A,C}:1.40513847116;HIC1:1.31105079078;MED-1{core}:1.30463449407;TFAP2B:1.29705018936;POU6F1:1.28187940821;ZNF148:1.22778671672;GTF2I:1.2242285745;PAX6:1.21775999506;GATA4:1.21279719842;FOXM1:1.18084071155;FOX{F1,F2,J1}:1.13621634746;MYFfamily:1.13231817325;ATF6:1.08443081382;CDX1,2,4:0.980958589194;FOX{I1,J2}:0.977353080066;HMX1:0.951260868394;NR3C1:0.915552555352;TFAP4:0.875596755923;SOX5:0.871518726484;HMGA1,2:0.864941462929;EGR1..3:0.853071321553;RREB1:0.830396714929;ADNP_IRX_SIX_ZHX:0.76746501804;TLX1..3_NFIC{dimer}:0.754033857862;ZNF423:0.748703294938;KLF4:0.740733319254;PAX5:0.734497719607;GLI1..3:0.70711404082;ZNF384:0.682187218849;PITX1..3:0.681982415327;RBPJ:0.672149374115;TOPORS:0.664290227836;GCM1,2:0.653494589304;LMO2:0.635429670296;DMAP1_NCOR{1,2}_SMARC:0.619843979697;GFI1B:0.616204720529;FOXA2:0.581385353441;CDC5L:0.572563068833;NKX2-1,4:0.570737997596;REST:0.51365822469;BREu{core}:0.513378687311;NANOG:0.505067084883;ZFP161:0.503443049801;TBX4,5:0.479670834272;ESR1:0.477763227168;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.445436194414;TLX2:0.441731245489;AIRE:0.43723950399;GZF1:0.429957972387;STAT2,4,6:0.42871658779;ETS1,2:0.419707345702;NR5A1,2:0.404890749786;RXR{A,B,G}:0.398015363059;HBP1_HMGB_SSRP1_UBTF:0.38216244883;SMAD1..7,9:0.366898228539;FOXQ1:0.346184291509;NHLH1,2:0.303458841284;NKX6-1,2:0.296673129856;ZBTB16:0.29397817605;MYOD1:0.283713574434;ONECUT1,2:0.274304394335;LEF1_TCF7_TCF7L1,2:0.270652991381;IRF1,2:0.266366385871;PRRX1,2:0.264860811124;SREBF1,2:0.262662889797;FOXN1:0.250024411737;POU1F1:0.244389866355;TEAD1:0.238992918624;IRF7:0.236491033827;GFI1:0.222604034826;VSX1,2:0.208263903414;AR:0.177607199101;NANOG{mouse}:0.175305862636;OCT4_SOX2{dimer}:0.149752044949;GTF2A1,2:0.132352578058;TAL1_TCF{3,4,12}:0.129024875331;ATF2:0.124985083456;SPIB:0.11559387634;ATF4:0.0800809538856;MEF2{A,B,C,D}:0.0421905176269;EBF1:0.0397754858405;NKX2-2,8:0.038648093772;SPI1:0.0336800546134;ESRRA:0.0333479047093;NFATC1..3:-0.00630082737492;ARID5B:-0.00711431547617;ALX1:-0.00923576333128;CUX2:-0.022683158711;UFEwm:-0.0257256273908;STAT1,3:-0.0355782880885;ZBTB6:-0.0363911857766;HES1:-0.0657018756698;FOXP3:-0.0692220927696;SOX2:-0.0957178462632;MAFB:-0.102120632227;POU3F1..4:-0.102933697343;SOX17:-0.120676517407;RXRA_VDR{dimer}:-0.126436122184;POU2F1..3:-0.143264600463;IKZF1:-0.153465641654;CEBPA,B_DDIT3:-0.161090152309;SOX{8,9,10}:-0.182672154111;XBP1:-0.195369062919;RUNX1..3:-0.198735117386;HIF1A:-0.216720428499;ZIC1..3:-0.222411461719;TEF:-0.225369420059;bHLH_family:-0.242763111492;JUN:-0.251132671656;PAX2:-0.255735136584;ZNF238:-0.258133705221;LHX3,4:-0.291154964671;EVI1:-0.309668459;NFKB1_REL_RELA:-0.310313010291;PAX3,7:-0.351176652554;PBX1:-0.393671611483;TGIF1:-0.397953113667;ATF5_CREB3:-0.41646889202;HAND1,2:-0.425530577145;NFIL3:-0.464178212362;ZNF143:-0.478702295528;HLF:-0.479798578914;AHR_ARNT_ARNT2:-0.49893173281;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.50071967433;NFY{A,B,C}:-0.510441157692;FOSL2:-0.527330361871;NFIX:-0.561732019343;NFE2:-0.57686197585;ELF1,2,4:-0.581119500071;PPARG:-0.598214190793;NKX3-2:-0.604446657392;TFDP1:-0.611835991344;TP53:-0.615621654441;E2F1..5:-0.61594453459;CREB1:-0.625413055861;PDX1:-0.643677795292;RFX2..5_RFXANK_RFXAP:-0.676266140636;HOX{A4,D4}:-0.727175040251;FOS_FOS{B,L1}_JUN{B,D}:-0.759227175839;RFX1:-0.80487324359;NKX3-1:-0.844638067187;RORA:-0.844941402991;NRF1:-0.891548501044;CRX:-0.912743834992;NFE2L2:-0.973630430761;BACH2:-0.982125399229;HOX{A5,B5}:-1.07338808665;NFE2L1:-1.12924024331;PAX4:-1.19051072024;ALX4:-1.19693081161;HSF1,2:-1.2863252534;PAX1,9:-1.2864108292;MYB:-1.33801535546;STAT5{A,B}:-1.33862796405;EN1,2:-1.33943718228;HOXA9_MEIS1:-1.50050341398;YY1:-1.6560357995;ELK1,4_GABP{A,B1}:-1.67527325961;PAX8:-2.01552186177
}}
}}

Revision as of 14:01, 21 March 2012


Name:colon, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecolon
dev stage37 weeks fetus
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB207218
catalog numberCat:RtHFN: Colon
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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: CNhs11780



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: CNhs11780



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: CNhs11780


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
0000059 (large intestine)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001155 (colon)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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