Personal tools

FF:692-21D1: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:692-21D1
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000479,UBERON:0001062
|name=whole body, neonate N06
|sample_id=692
|rna_tube_id=21D1
|rna_box=21
|rna_position=D1
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_dev_stage=6 days neonate
|sample_tissue=whole body
|sample_donor(cell lot)=
|sample_sex=mixture
|sample_age=
|sample_ethnicity=
|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=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=
|rna_concentration=
|sample_note=
|profile_hcage=CNhs10515,LSID649,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000479,UBERON:0001062
|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=TBP:3.61580461955;HOX{A4,D4}:2.56527698743;SMAD1..7,9:2.51043625328;FOXL1:2.37666021884;ALX1:2.35807434858;ESR1:2.29781351319;MEF2{A,B,C,D}:2.27814580608;TFCP2:2.27396124057;TFAP4:2.23526176882;GLI1..3:2.08749725989;GCM1,2:2.04568872473;ZNF148:1.97034539092;MYOD1:1.90043073937;FOSL2:1.88269826869;TFAP2{A,C}:1.84912224615;ZNF238:1.78143010192;PAX1,9:1.71473425355;NFE2L2:1.691751673;EBF1:1.55250942437;FOXP3:1.50153870557;NFATC1..3:1.44670847242;MYFfamily:1.44028181279;TAL1_TCF{3,4,12}:1.40161132358;FOX{I1,J2}:1.39886773112;LEF1_TCF7_TCF7L1,2:1.33450696238;TEAD1:1.27610322224;FOS_FOS{B,L1}_JUN{B,D}:1.27414279606;TLX2:1.27074726117;NKX2-3_NKX2-5:1.17255486488;SOX5:1.14017589898;ATF6:1.13894691507;TLX1..3_NFIC{dimer}:1.12285225247;TOPORS:1.10921338842;XCPE1{core}:1.10729380464;MAFB:1.09121873801;PAX5:1.08392103529;SRF:1.07430811796;RXRA_VDR{dimer}:1.04672067235;TGIF1:1.04503390897;ZNF423:1.02653879844;GTF2A1,2:0.994385344886;MAZ:0.981977124436;VSX1,2:0.968598576242;IKZF1:0.957817388718;MTF1:0.956323540724;NANOG:0.950495047453;TP53:0.932742876775;STAT2,4,6:0.923083630548;SP1:0.919232079337;NHLH1,2:0.916149302991;SOX{8,9,10}:0.888195948508;EN1,2:0.86002782377;EP300:0.856784967501;HES1:0.848739318754;CEBPA,B_DDIT3:0.826103348416;GTF2I:0.804701346143;MYBL2:0.788982153925;PATZ1:0.769097179357;FOXA2:0.763323697059;HMX1:0.744489703447;BACH2:0.731290525331;HSF1,2:0.714613927982;GFI1B:0.675025034873;HLF:0.653690009554;KLF4:0.623352087305;NR5A1,2:0.612951553773;PPARG:0.611490058718;HIC1:0.590992893397;NFE2L1:0.573792341751;GFI1:0.556598688547;TBX4,5:0.554181184386;LMO2:0.552568318889;RXR{A,B,G}:0.481398231355;RREB1:0.477872518267;TFAP2B:0.470326610669;ESRRA:0.466800757998;NKX2-1,4:0.435643925329;NR3C1:0.427056741687;T:0.414399700214;GATA6:0.395715772772;CRX:0.378605416167;PAX2:0.375177351891;NFE2:0.369873907228;ZIC1..3:0.368380972611;PRDM1:0.333875223893;SPZ1:0.330395401771;RORA:0.330311013683;NKX3-2:0.30043788695;RUNX1..3:0.285006108358;ZBTB6:0.27491407879;MTE{core}:0.266657006608;REST:0.262668198745;HIF1A:0.252694532018;HMGA1,2:0.252333583838;SREBF1,2:0.23669556674;GATA4:0.183432397482;MZF1:0.176700483548;SPI1:0.166151320184;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.162611619942;GZF1:0.158727117553;FOX{F1,F2,J1}:0.152892320742;SNAI1..3:0.130863473289;SPIB:0.107536107508;NR1H4:0.106318151918;STAT5{A,B}:0.10382434826;DMAP1_NCOR{1,2}_SMARC:0.0930439203393;IRF7:0.0924498935544;ALX4:0.0636833581989;PDX1:0.0625871875495;EGR1..3:0.0567594034772;UFEwm:0.052625645516;ETS1,2:0.0494824480689;ATF2:0.0470362848986;IKZF2:0.0351162933459;POU3F1..4:0.0187596334328;HOXA9_MEIS1:0.0123830502205;NKX2-2,8:0.0109314651948;FOX{D1,D2}:-0.0453895329073;NFIL3:-0.0555420767264;NFKB1_REL_RELA:-0.115280268584;POU2F1..3:-0.15987066058;SOX2:-0.163903261414;MED-1{core}:-0.186939034467;YY1:-0.188368129428;POU5F1:-0.189752344197;HOX{A5,B5}:-0.192342986033;FOXQ1:-0.204018592509;PRRX1,2:-0.206104571411;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.21614412786;E2F1..5:-0.217407013529;ZFP161:-0.22113980061;HNF1A:-0.226477543642;FOXO1,3,4:-0.234734318039;CUX2:-0.269273986785;HNF4A_NR2F1,2:-0.27535791591;JUN:-0.279540135945;ZEB1:-0.30018227749;NANOG{mouse}:-0.302769074931;IRF1,2:-0.317599189792;HAND1,2:-0.322019767274;BREu{core}:-0.326726995675;SOX17:-0.329939157907;EVI1:-0.351675971179;ATF4:-0.406139785367;DBP:-0.429115099094;LHX3,4:-0.430114132624;FOXN1:-0.437695938817;TFDP1:-0.451824220219;NR6A1:-0.455547152616;POU6F1:-0.463859384762;FOXM1:-0.467093613767;ZNF143:-0.469951848796;NKX3-1:-0.485301241081;MYB:-0.532378007106;TEF:-0.536784681494;NFIX:-0.547955864037;RFX1:-0.568958261668;ZNF384:-0.587797242908;bHLH_family:-0.594375410944;PAX6:-0.601134817031;ELF1,2,4:-0.607407536778;RBPJ:-0.681561602125;RFX2..5_RFXANK_RFXAP:-0.701783443504;AR:-0.732091263483;CDC5L:-0.776548359213;NFY{A,B,C}:-0.850165909163;ATF5_CREB3:-0.850934526498;AHR_ARNT_ARNT2:-0.873281179786;PBX1:-0.885913781914;HBP1_HMGB_SSRP1_UBTF:-0.887009910426;PITX1..3:-0.909852357574;PAX4:-0.911198190091;FOXP1:-0.991114423879;NRF1:-0.991961786386;OCT4_SOX2{dimer}:-1.00163416311;PAX8:-1.028836624;BPTF:-1.15176776487;NKX6-1,2:-1.1585524407;STAT1,3:-1.19364342198;ADNP_IRX_SIX_ZHX:-1.21235327903;CREB1:-1.2135722232;POU1F1:-1.28116879681;AIRE:-1.32647117626;ARID5B:-1.38000094947;FOXD3:-1.44673878613;ELK1,4_GABP{A,B1}:-1.47138434406;ONECUT1,2:-1.65775264557;CDX1,2,4:-1.73968725906;ZBTB16:-1.91133068796
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:692-21D1
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011405
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011405
|name=whole body, neonate N06
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10515,LSID649,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=21
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=D1
|rna_rin=
|rna_sample_type=
|rna_tube_id=21D1
|rna_weight_ug=
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=
|sample_description=
|sample_dev_stage=6 days neonate
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=692
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=whole body
|top_motifs=TBP:3.61580461955;HOX{A4,D4}:2.56527698743;SMAD1..7,9:2.51043625328;FOXL1:2.37666021884;ALX1:2.35807434858;ESR1:2.29781351319;MEF2{A,B,C,D}:2.27814580608;TFCP2:2.27396124057;TFAP4:2.23526176882;GLI1..3:2.08749725989;GCM1,2:2.04568872473;ZNF148:1.97034539092;MYOD1:1.90043073937;FOSL2:1.88269826869;TFAP2{A,C}:1.84912224615;ZNF238:1.78143010192;PAX1,9:1.71473425355;NFE2L2:1.691751673;EBF1:1.55250942437;FOXP3:1.50153870557;NFATC1..3:1.44670847242;MYFfamily:1.44028181279;TAL1_TCF{3,4,12}:1.40161132358;FOX{I1,J2}:1.39886773112;LEF1_TCF7_TCF7L1,2:1.33450696238;TEAD1:1.27610322224;FOS_FOS{B,L1}_JUN{B,D}:1.27414279606;TLX2:1.27074726117;NKX2-3_NKX2-5:1.17255486488;SOX5:1.14017589898;ATF6:1.13894691507;TLX1..3_NFIC{dimer}:1.12285225247;TOPORS:1.10921338842;XCPE1{core}:1.10729380464;MAFB:1.09121873801;PAX5:1.08392103529;SRF:1.07430811796;RXRA_VDR{dimer}:1.04672067235;TGIF1:1.04503390897;ZNF423:1.02653879844;GTF2A1,2:0.994385344886;MAZ:0.981977124436;VSX1,2:0.968598576242;IKZF1:0.957817388718;MTF1:0.956323540724;NANOG:0.950495047453;TP53:0.932742876775;STAT2,4,6:0.923083630548;SP1:0.919232079337;NHLH1,2:0.916149302991;SOX{8,9,10}:0.888195948508;EN1,2:0.86002782377;EP300:0.856784967501;HES1:0.848739318754;CEBPA,B_DDIT3:0.826103348416;GTF2I:0.804701346143;MYBL2:0.788982153925;PATZ1:0.769097179357;FOXA2:0.763323697059;HMX1:0.744489703447;BACH2:0.731290525331;HSF1,2:0.714613927982;GFI1B:0.675025034873;HLF:0.653690009554;KLF4:0.623352087305;NR5A1,2:0.612951553773;PPARG:0.611490058718;HIC1:0.590992893397;NFE2L1:0.573792341751;GFI1:0.556598688547;TBX4,5:0.554181184386;LMO2:0.552568318889;RXR{A,B,G}:0.481398231355;RREB1:0.477872518267;TFAP2B:0.470326610669;ESRRA:0.466800757998;NKX2-1,4:0.435643925329;NR3C1:0.427056741687;T:0.414399700214;GATA6:0.395715772772;CRX:0.378605416167;PAX2:0.375177351891;NFE2:0.369873907228;ZIC1..3:0.368380972611;PRDM1:0.333875223893;SPZ1:0.330395401771;RORA:0.330311013683;NKX3-2:0.30043788695;RUNX1..3:0.285006108358;ZBTB6:0.27491407879;MTE{core}:0.266657006608;REST:0.262668198745;HIF1A:0.252694532018;HMGA1,2:0.252333583838;SREBF1,2:0.23669556674;GATA4:0.183432397482;MZF1:0.176700483548;SPI1:0.166151320184;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.162611619942;GZF1:0.158727117553;FOX{F1,F2,J1}:0.152892320742;SNAI1..3:0.130863473289;SPIB:0.107536107508;NR1H4:0.106318151918;STAT5{A,B}:0.10382434826;DMAP1_NCOR{1,2}_SMARC:0.0930439203393;IRF7:0.0924498935544;ALX4:0.0636833581989;PDX1:0.0625871875495;EGR1..3:0.0567594034772;UFEwm:0.052625645516;ETS1,2:0.0494824480689;ATF2:0.0470362848986;IKZF2:0.0351162933459;POU3F1..4:0.0187596334328;HOXA9_MEIS1:0.0123830502205;NKX2-2,8:0.0109314651948;FOX{D1,D2}:-0.0453895329073;NFIL3:-0.0555420767264;NFKB1_REL_RELA:-0.115280268584;POU2F1..3:-0.15987066058;SOX2:-0.163903261414;MED-1{core}:-0.186939034467;YY1:-0.188368129428;POU5F1:-0.189752344197;HOX{A5,B5}:-0.192342986033;FOXQ1:-0.204018592509;PRRX1,2:-0.206104571411;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.21614412786;E2F1..5:-0.217407013529;ZFP161:-0.22113980061;HNF1A:-0.226477543642;FOXO1,3,4:-0.234734318039;CUX2:-0.269273986785;HNF4A_NR2F1,2:-0.27535791591;JUN:-0.279540135945;ZEB1:-0.30018227749;NANOG{mouse}:-0.302769074931;IRF1,2:-0.317599189792;HAND1,2:-0.322019767274;BREu{core}:-0.326726995675;SOX17:-0.329939157907;EVI1:-0.351675971179;ATF4:-0.406139785367;DBP:-0.429115099094;LHX3,4:-0.430114132624;FOXN1:-0.437695938817;TFDP1:-0.451824220219;NR6A1:-0.455547152616;POU6F1:-0.463859384762;FOXM1:-0.467093613767;ZNF143:-0.469951848796;NKX3-1:-0.485301241081;MYB:-0.532378007106;TEF:-0.536784681494;NFIX:-0.547955864037;RFX1:-0.568958261668;ZNF384:-0.587797242908;bHLH_family:-0.594375410944;PAX6:-0.601134817031;ELF1,2,4:-0.607407536778;RBPJ:-0.681561602125;RFX2..5_RFXANK_RFXAP:-0.701783443504;AR:-0.732091263483;CDC5L:-0.776548359213;NFY{A,B,C}:-0.850165909163;ATF5_CREB3:-0.850934526498;AHR_ARNT_ARNT2:-0.873281179786;PBX1:-0.885913781914;HBP1_HMGB_SSRP1_UBTF:-0.887009910426;PITX1..3:-0.909852357574;PAX4:-0.911198190091;FOXP1:-0.991114423879;NRF1:-0.991961786386;OCT4_SOX2{dimer}:-1.00163416311;PAX8:-1.028836624;BPTF:-1.15176776487;NKX6-1,2:-1.1585524407;STAT1,3:-1.19364342198;ADNP_IRX_SIX_ZHX:-1.21235327903;CREB1:-1.2135722232;POU1F1:-1.28116879681;AIRE:-1.32647117626;ARID5B:-1.38000094947;FOXD3:-1.44673878613;ELK1,4_GABP{A,B1}:-1.47138434406;ONECUT1,2:-1.65775264557;CDX1,2,4:-1.73968725906;ZBTB16:-1.91133068796
}}
}}

Revision as of 15:36, 21 March 2012


Name:whole body, neonate N06
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage6 days neonate
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
CollapseMm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
CollapseMm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} 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

CNhs10515



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: CNhs10515



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: CNhs10515



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: CNhs10515


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)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0001062 (anatomical entity)

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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:692-21D1&oldid=729100"