FF:12237-129G5: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
{{f5samples | {{f5samples | ||
|DRA_sample_Accession=CAGE@SAMD00006009 | |DRA_sample_Accession=CAGE@SAMD00006009 | ||
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00006009 | |||
|accession_numbers=CAGE;DRX008539;DRR009411;DRZ000836;DRZ002221;DRZ012186;DRZ013571 | |accession_numbers=CAGE;DRX008539;DRR009411;DRZ000836;DRZ002221;DRZ012186;DRZ013571 | ||
|accession_numbers_RNASeq=sRNA-Seq;DRX037012;DRR041378;DRZ007020 | |||
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000305,UBERON:0002384,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0004923,UBERON:0005631,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000478,UBERON:0010317,UBERON:0000158 | |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000305,UBERON:0002384,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0004923,UBERON:0005631,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000478,UBERON:0010317,UBERON:0000158 | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0000548,CL:0002320,CL:0002371,CL:0000219,CL:0000134,CL:0000349,CL:0000255,CL:0000034,CL:0002537 | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0000548,CL:0002320,CL:0002371,CL:0000219,CL:0000134,CL:0000349,CL:0000255,CL:0000034,CL:0002537 | ||
| Line 80: | Line 82: | ||
|rna_tube_id=129G5 | |rna_tube_id=129G5 | ||
|rna_weight_ug=16.46892 | |rna_weight_ug=16.46892 | ||
|rnaseq_library_id=SRhi10003.TTAGGC | |||
|sample_age= | |sample_age= | ||
|sample_category=primary cells | |sample_category=primary cells | ||
| Line 103: | Line 106: | ||
|top_motifs=FOXL1:2.31664437587;PAX4:2.19483939877;NKX2-1,4:2.12953346534;HAND1,2:2.02299095803;SNAI1..3:1.98896591685;HOX{A6,A7,B6,B7}:1.98704421016;EP300:1.9334910447;FOXM1:1.91994503774;ZEB1:1.77760281958;RORA:1.70825824866;NKX2-2,8:1.56722281265;CDC5L:1.5468868799;FOXO1,3,4:1.49823769421;FOXN1:1.46877515309;HIF1A:1.46276468348;XCPE1{core}:1.43037381255;ZNF148:1.29929070134;TEAD1:1.26659912725;AIRE:1.25855184483;FOX{I1,J2}:1.21039851511;POU6F1:1.20935148872;SP1:1.10166432227;HMGA1,2:1.05471077744;TEF:1.00983236428;ARID5B:0.987920395602;MAZ:0.940203042252;PPARG:0.920504335992;POU3F1..4:0.911340086924;TBX4,5:0.8987396591;GLI1..3:0.891614262353;FOS_FOS{B,L1}_JUN{B,D}:0.871473418347;TP53:0.854819703128;TLX2:0.774979251224;FOX{D1,D2}:0.751496389477;CRX:0.747160206813;PAX8:0.686288193013;TFAP2{A,C}:0.631026384335;PAX5:0.622039597351;MYOD1:0.612664509964;BACH2:0.606768144529;GCM1,2:0.597345902457;ONECUT1,2:0.595016274021;UFEwm:0.581638540584;ZNF384:0.559227623279;STAT1,3:0.502795232433;RXRA_VDR{dimer}:0.481861483377;IKZF1:0.479123304428;TBP:0.469838683651;ALX1:0.45980531434;HOX{A5,B5}:0.451455347093;ADNP_IRX_SIX_ZHX:0.438983736026;ZIC1..3:0.404971707214;POU1F1:0.400057119706;BPTF:0.374784592199;FOXQ1:0.361786212001;FOSL2:0.361736647448;FOXA2:0.358378515188;RFX1:0.318769144457;LEF1_TCF7_TCF7L1,2:0.316721383938;PAX1,9:0.306583477645;VSX1,2:0.305980777181;ZNF238:0.295692153516;CREB1:0.258044054323;HLF:0.25221005401;NFATC1..3:0.248665006526;NFIL3:0.244997051001;MTF1:0.237027176488;PITX1..3:0.216430016946;TFCP2:0.211465843433;ESR1:0.201497322947;NKX2-3_NKX2-5:0.190497247818;JUN:0.182515903093;MED-1{core}:0.178325007391;bHLH_family:0.176350066918;NR3C1:0.176283125338;DBP:0.175366395951;GTF2I:0.128024378998;HOXA9_MEIS1:0.105493969854;ZBTB6:0.101339138981;PAX2:0.0820453280066;HBP1_HMGB_SSRP1_UBTF:0.0673433472273;EVI1:0.0550102854654;HMX1:0.0117837373067;NRF1:0.0114859717235;EBF1:-0.00539253530439;HOX{A4,D4}:-0.0177746939063;SOX5:-0.0181870891671;ELK1,4_GABP{A,B1}:-0.0283591125945;GATA6:-0.0417042416454;GZF1:-0.0430442290473;NKX3-2:-0.047630160683;POU2F1..3:-0.0637146524054;ATF5_CREB3:-0.086858742427;ZNF143:-0.0917137290203;HSF1,2:-0.105571543355;KLF4:-0.107629122309;ZBTB16:-0.110008683164;NFE2:-0.123568015097;SREBF1,2:-0.141505968582;TLX1..3_NFIC{dimer}:-0.150813593537;ATF6:-0.153574029416;MYBL2:-0.167379310462;RFX2..5_RFXANK_RFXAP:-0.196839915718;ATF4:-0.204022907772;PAX3,7:-0.210683992222;EGR1..3:-0.213256678358;HNF1A:-0.225625512789;XBP1:-0.226579194543;ALX4:-0.235758690724;FOXP3:-0.237476678191;NR1H4:-0.26765478273;SOX17:-0.268119775413;MZF1:-0.285894840342;MEF2{A,B,C,D}:-0.305248671967;HIC1:-0.392738023359;RREB1:-0.402197210837;REST:-0.403348872688;GFI1:-0.413105484152;IKZF2:-0.413678441676;STAT5{A,B}:-0.416662886097;MTE{core}:-0.428936626685;ATF2:-0.439388967026;EN1,2:-0.439873935039;FOXP1:-0.441816669224;PATZ1:-0.450820199224;AHR_ARNT_ARNT2:-0.465813245287;ESRRA:-0.472461781683;MYFfamily:-0.488232429936;PBX1:-0.492779001981;IRF7:-0.502064699745;NFKB1_REL_RELA:-0.515586009133;ZNF423:-0.531142060197;OCT4_SOX2{dimer}:-0.544065162735;MYB:-0.544345641389;LMO2:-0.551722751539;RXR{A,B,G}:-0.567192279908;HNF4A_NR2F1,2:-0.56786226601;NHLH1,2:-0.569658788552;AR:-0.583388908689;SMAD1..7,9:-0.604592612466;SPI1:-0.631804884385;TFAP2B:-0.632819663431;NFY{A,B,C}:-0.640085499405;NR5A1,2:-0.640470001441;SOX2:-0.645190360297;DMAP1_NCOR{1,2}_SMARC:-0.647051799469;NKX6-1,2:-0.648671265025;ETS1,2:-0.659530491859;FOX{F1,F2,J1}:-0.675026056593;GTF2A1,2:-0.678899286012;PAX6:-0.687056912911;RBPJ:-0.701872123716;YY1:-0.702391808584;ELF1,2,4:-0.713281239517;CEBPA,B_DDIT3:-0.728137120872;CUX2:-0.74712544523;SOX{8,9,10}:-0.751337594089;ZFP161:-0.760406467288;HES1:-0.773419758489;PDX1:-0.778630261248;NANOG{mouse}:-0.787670486137;GFI1B:-0.789862897975;LHX3,4:-0.795500833026;IRF1,2:-0.809249125694;SPIB:-0.845155157739;RUNX1..3:-0.858924132209;GATA4:-0.886261001639;SRF:-0.919349607824;TFAP4:-0.930297596785;STAT2,4,6:-0.949780555859;TGIF1:-0.955424103992;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.986366454384;E2F1..5:-1.01337682704;NR6A1:-1.02698799803;TOPORS:-1.0314759649;MAFB:-1.05877844872;NFE2L2:-1.06512587115;PRDM1:-1.09496282954;TFDP1:-1.18474388378;BREu{core}:-1.19237128596;SPZ1:-1.21480286586;PRRX1,2:-1.22082045137;FOXD3:-1.23233405579;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.27779591958;CDX1,2,4:-1.28804464076;T:-1.29391327354;TAL1_TCF{3,4,12}:-1.36707342871;NANOG:-1.44701866391;NFE2L1:-1.52787141609;NKX3-1:-1.63109746664;POU5F1:-1.72580579526;NFIX:-1.91133180355 | |top_motifs=FOXL1:2.31664437587;PAX4:2.19483939877;NKX2-1,4:2.12953346534;HAND1,2:2.02299095803;SNAI1..3:1.98896591685;HOX{A6,A7,B6,B7}:1.98704421016;EP300:1.9334910447;FOXM1:1.91994503774;ZEB1:1.77760281958;RORA:1.70825824866;NKX2-2,8:1.56722281265;CDC5L:1.5468868799;FOXO1,3,4:1.49823769421;FOXN1:1.46877515309;HIF1A:1.46276468348;XCPE1{core}:1.43037381255;ZNF148:1.29929070134;TEAD1:1.26659912725;AIRE:1.25855184483;FOX{I1,J2}:1.21039851511;POU6F1:1.20935148872;SP1:1.10166432227;HMGA1,2:1.05471077744;TEF:1.00983236428;ARID5B:0.987920395602;MAZ:0.940203042252;PPARG:0.920504335992;POU3F1..4:0.911340086924;TBX4,5:0.8987396591;GLI1..3:0.891614262353;FOS_FOS{B,L1}_JUN{B,D}:0.871473418347;TP53:0.854819703128;TLX2:0.774979251224;FOX{D1,D2}:0.751496389477;CRX:0.747160206813;PAX8:0.686288193013;TFAP2{A,C}:0.631026384335;PAX5:0.622039597351;MYOD1:0.612664509964;BACH2:0.606768144529;GCM1,2:0.597345902457;ONECUT1,2:0.595016274021;UFEwm:0.581638540584;ZNF384:0.559227623279;STAT1,3:0.502795232433;RXRA_VDR{dimer}:0.481861483377;IKZF1:0.479123304428;TBP:0.469838683651;ALX1:0.45980531434;HOX{A5,B5}:0.451455347093;ADNP_IRX_SIX_ZHX:0.438983736026;ZIC1..3:0.404971707214;POU1F1:0.400057119706;BPTF:0.374784592199;FOXQ1:0.361786212001;FOSL2:0.361736647448;FOXA2:0.358378515188;RFX1:0.318769144457;LEF1_TCF7_TCF7L1,2:0.316721383938;PAX1,9:0.306583477645;VSX1,2:0.305980777181;ZNF238:0.295692153516;CREB1:0.258044054323;HLF:0.25221005401;NFATC1..3:0.248665006526;NFIL3:0.244997051001;MTF1:0.237027176488;PITX1..3:0.216430016946;TFCP2:0.211465843433;ESR1:0.201497322947;NKX2-3_NKX2-5:0.190497247818;JUN:0.182515903093;MED-1{core}:0.178325007391;bHLH_family:0.176350066918;NR3C1:0.176283125338;DBP:0.175366395951;GTF2I:0.128024378998;HOXA9_MEIS1:0.105493969854;ZBTB6:0.101339138981;PAX2:0.0820453280066;HBP1_HMGB_SSRP1_UBTF:0.0673433472273;EVI1:0.0550102854654;HMX1:0.0117837373067;NRF1:0.0114859717235;EBF1:-0.00539253530439;HOX{A4,D4}:-0.0177746939063;SOX5:-0.0181870891671;ELK1,4_GABP{A,B1}:-0.0283591125945;GATA6:-0.0417042416454;GZF1:-0.0430442290473;NKX3-2:-0.047630160683;POU2F1..3:-0.0637146524054;ATF5_CREB3:-0.086858742427;ZNF143:-0.0917137290203;HSF1,2:-0.105571543355;KLF4:-0.107629122309;ZBTB16:-0.110008683164;NFE2:-0.123568015097;SREBF1,2:-0.141505968582;TLX1..3_NFIC{dimer}:-0.150813593537;ATF6:-0.153574029416;MYBL2:-0.167379310462;RFX2..5_RFXANK_RFXAP:-0.196839915718;ATF4:-0.204022907772;PAX3,7:-0.210683992222;EGR1..3:-0.213256678358;HNF1A:-0.225625512789;XBP1:-0.226579194543;ALX4:-0.235758690724;FOXP3:-0.237476678191;NR1H4:-0.26765478273;SOX17:-0.268119775413;MZF1:-0.285894840342;MEF2{A,B,C,D}:-0.305248671967;HIC1:-0.392738023359;RREB1:-0.402197210837;REST:-0.403348872688;GFI1:-0.413105484152;IKZF2:-0.413678441676;STAT5{A,B}:-0.416662886097;MTE{core}:-0.428936626685;ATF2:-0.439388967026;EN1,2:-0.439873935039;FOXP1:-0.441816669224;PATZ1:-0.450820199224;AHR_ARNT_ARNT2:-0.465813245287;ESRRA:-0.472461781683;MYFfamily:-0.488232429936;PBX1:-0.492779001981;IRF7:-0.502064699745;NFKB1_REL_RELA:-0.515586009133;ZNF423:-0.531142060197;OCT4_SOX2{dimer}:-0.544065162735;MYB:-0.544345641389;LMO2:-0.551722751539;RXR{A,B,G}:-0.567192279908;HNF4A_NR2F1,2:-0.56786226601;NHLH1,2:-0.569658788552;AR:-0.583388908689;SMAD1..7,9:-0.604592612466;SPI1:-0.631804884385;TFAP2B:-0.632819663431;NFY{A,B,C}:-0.640085499405;NR5A1,2:-0.640470001441;SOX2:-0.645190360297;DMAP1_NCOR{1,2}_SMARC:-0.647051799469;NKX6-1,2:-0.648671265025;ETS1,2:-0.659530491859;FOX{F1,F2,J1}:-0.675026056593;GTF2A1,2:-0.678899286012;PAX6:-0.687056912911;RBPJ:-0.701872123716;YY1:-0.702391808584;ELF1,2,4:-0.713281239517;CEBPA,B_DDIT3:-0.728137120872;CUX2:-0.74712544523;SOX{8,9,10}:-0.751337594089;ZFP161:-0.760406467288;HES1:-0.773419758489;PDX1:-0.778630261248;NANOG{mouse}:-0.787670486137;GFI1B:-0.789862897975;LHX3,4:-0.795500833026;IRF1,2:-0.809249125694;SPIB:-0.845155157739;RUNX1..3:-0.858924132209;GATA4:-0.886261001639;SRF:-0.919349607824;TFAP4:-0.930297596785;STAT2,4,6:-0.949780555859;TGIF1:-0.955424103992;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.986366454384;E2F1..5:-1.01337682704;NR6A1:-1.02698799803;TOPORS:-1.0314759649;MAFB:-1.05877844872;NFE2L2:-1.06512587115;PRDM1:-1.09496282954;TFDP1:-1.18474388378;BREu{core}:-1.19237128596;SPZ1:-1.21480286586;PRRX1,2:-1.22082045137;FOXD3:-1.23233405579;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.27779591958;CDX1,2,4:-1.28804464076;T:-1.29391327354;TAL1_TCF{3,4,12}:-1.36707342871;NANOG:-1.44701866391;NFE2L1:-1.52787141609;NKX3-1:-1.63109746664;POU5F1:-1.72580579526;NFIX:-1.91133180355 | ||
|xref= | |xref= | ||
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:12237-129G5;search_select_hide=table117:FF:12237-129G5 | |||
}} | }} | ||
Latest revision as of 18:36, 4 June 2020
| Name: | amniotic membrane cells, donor3 |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | CNhs12379 |
| Sample type: | primary cells |
| Genomic View: | UCSC |
| RefEX: | Specific genes |
| FANTOM CAT: | 1, 2, 3, 4, 5 |
| CAGEd-oPOSSUM: | link |
| ZENBU report : | link |
| ExpandAdditional information |
|---|
| ExpandCAGE Accession numbers |
|---|
| ExpandDownload raw sequence, BAM & CTSS |
|---|
| ExpandRNA-Seq Accession numbers |
|---|
Relative expression to median (log10)
Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
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
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: CNhs12379
| MA0090.1 |  | 1.00e-7 |
| MA0061.1 |  | 1.32e-2 |
| MA0055.1 |  | 1.34e-1 |
| MA0164.1 |  | 1.45e-1 |
| MA0141.1 |  | 1.49e-1 |
| Jaspar motif | Logo | p-value |
|---|
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: CNhs12379
| 109 |  | 1.01e-3 |
| 151 |  | 1.08e-1 |
| 130 |  | 1.12e-1 |
| 133 |  | 1.23e-2 |
| 164 |  | 1.24e-1 |
| Novel motif | Logo | p-value |
|---|
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: CNhs12379
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000010 human amniotic membrane cell- Amnion 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
CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000349 (extraembryonic cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002537 (amnion mesenchymal stem cell)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000305 (amnion)
0002384 (connective tissue)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0004923 (organ component layer)
0005631 (extraembryonic membrane)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000478 (extraembryonic structure)
0010317 (germ layer / neural crest derived structure)
0000158 (membranous layer)
FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000092 (human amniotic membrane cell sample)
0000101 (sample by species)
0000001 (sample)
0000010 (human amniotic membrane cell- Amnion sample)
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
CL:0000134 (mesenchymal cell)
