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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004853
|DRA_sample_Accession=CAGE@SAMD00004853
|accession_numbers=CAGE;DRX008934;DRR009808;DRZ001233;DRZ002616
|accession_numbers=CAGE;DRX008934;DRR009808;DRZ001233;DRZ002616;DRZ012583;DRZ013966
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000305,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:0007023,UBERON:0000305,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=
|ancestors_in_cell_lineage_facet=
Line 46: Line 46:
|library_id=CNhs10488
|library_id=CNhs10488
|library_id_phase_based=2:CNhs10488
|library_id_phase_based=2:CNhs10488
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;583
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;583
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/amnion%252c%2520adult%2520pregnant%2520day17%252e5.CNhs10488.583-22A8.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/amnion%252c%2520adult%2520pregnant%2520day17%252e5.CNhs10488.583-22A8.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/amnion%252c%2520adult%2520pregnant%2520day17%252e5.CNhs10488.583-22A8.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/amnion%252c%2520adult%2520pregnant%2520day17%252e5.CNhs10488.583-22A8.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/amnion%252c%2520adult%2520pregnant%2520day17%252e5.CNhs10488.583-22A8.mm9.nobarcode.rdna.fa.gz
|name=amnion, adult pregnant day17.5
|name=amnion, adult pregnant day17.5
|namespace=FANTOM5
|namespace=FANTOM5
Line 88: Line 97:
|top_motifs=FOXM1:3.26139085194;STAT2,4,6:3.12615293939;FOSL2:3.07917790283;NANOG{mouse}:2.45856337102;FOX{D1,D2}:2.35161948343;RXRA_VDR{dimer}:2.19017474479;BPTF:2.1258536594;AR:2.05922538338;BACH2:1.86344027449;SREBF1,2:1.81840793115;FOS_FOS{B,L1}_JUN{B,D}:1.76820706611;XCPE1{core}:1.66006417954;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.65496408165;SP1:1.61002946614;STAT5{A,B}:1.56896582612;TEAD1:1.55350140877;FOX{F1,F2,J1}:1.44909966945;FOXO1,3,4:1.43998090984;IKZF1:1.34861455648;FOXN1:1.34124412107;TFCP2:1.30083859395;PAX2:1.29196644022;SNAI1..3:1.26830577064;HNF1A:1.24834145914;HNF4A_NR2F1,2:1.24782498961;ZNF148:1.23033625658;HIF1A:1.22898733078;GLI1..3:1.2282593652;EBF1:1.20551802519;GZF1:1.20440574878;NFE2:1.14682803488;TBX4,5:1.04296331687;ZEB1:1.04232493321;PAX1,9:0.958632673023;TP53:0.878946289404;CEBPA,B_DDIT3:0.85882746505;ZNF423:0.852914156971;FOXA2:0.848871611271;MAFB:0.834197322476;ARID5B:0.832448918165;ATF4:0.770072048712;ESR1:0.735305591566;PDX1:0.727822471236;NKX3-2:0.717924879004;NFE2L2:0.710223647645;ATF6:0.647451338211;SPZ1:0.644826944884;MAZ:0.524605021423;PITX1..3:0.497871918084;HLF:0.492708631187;NR1H4:0.425715480645;EN1,2:0.42275975199;HAND1,2:0.412882094616;HMX1:0.39580120738;EP300:0.338644311245;GFI1B:0.303458289885;SRF:0.224052640093;NFKB1_REL_RELA:0.22126900883;EVI1:0.210724459188;ALX4:0.207511630955;TBP:0.176292621242;ETS1,2:0.166807759948;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.162545034462;FOXP1:0.135612971341;ESRRA:0.133796238539;PAX5:0.119941776222;T:0.111895641239;ELK1,4_GABP{A,B1}:0.104500333871;ZIC1..3:0.0988733580815;NR6A1:0.0968171788804;NFE2L1:0.0833859759281;PAX4:0.076398958209;MTE{core}:0.0758758215672;SOX5:0.0739279835355;TFAP2{A,C}:0.0545318101567;STAT1,3:0.0529629266931;ELF1,2,4:0.0431192527781;HMGA1,2:0.0413035080675;IRF1,2:0.0375082538977;MYOD1:0.0272373423745;HOXA9_MEIS1:-0.0131458404838;GCM1,2:-0.0382647603009;RXR{A,B,G}:-0.0439440470419;GTF2I:-0.0760584516978;IKZF2:-0.0772928869952;CREB1:-0.104852092732;EGR1..3:-0.10590608331;TOPORS:-0.111847210426;RREB1:-0.138884646756;ATF2:-0.153155390161;PATZ1:-0.155467459929;SPIB:-0.198353438166;SPI1:-0.200902287523;TLX1..3_NFIC{dimer}:-0.207207355993;FOXQ1:-0.233643342134;DBP:-0.249508923964;AIRE:-0.252127842161;CRX:-0.256680111627;TFAP2B:-0.259734373553;NHLH1,2:-0.275905440298;MYBL2:-0.282316631275;TAL1_TCF{3,4,12}:-0.282615716291;REST:-0.309852750607;TGIF1:-0.309868677434;UFEwm:-0.33518221182;GATA6:-0.354519909419;RBPJ:-0.386041287177;MEF2{A,B,C,D}:-0.391822407381;MYFfamily:-0.409368750679;NFATC1..3:-0.424337139338;ZBTB6:-0.43877103741;NFIL3:-0.453738862673;HBP1_HMGB_SSRP1_UBTF:-0.456418676624;MED-1{core}:-0.469379976592;ATF5_CREB3:-0.499740536008;TFAP4:-0.502851669051;NKX2-3_NKX2-5:-0.526815378381;HIC1:-0.533070663224;FOXP3:-0.539584414591;DMAP1_NCOR{1,2}_SMARC:-0.543468450547;NKX3-1:-0.561232811429;CDX1,2,4:-0.580052456661;ZNF238:-0.591794851959;bHLH_family:-0.653973085355;LHX3,4:-0.661414330967;IRF7:-0.678302403169;MYB:-0.691356959269;ZNF143:-0.693627295401;ZFP161:-0.705224321805;CUX2:-0.707460210039;AHR_ARNT_ARNT2:-0.722505150136;RUNX1..3:-0.75925870364;ONECUT1,2:-0.770828497778;LMO2:-0.777117516479;RFX1:-0.778801272361;GTF2A1,2:-0.780249520574;MTF1:-0.784068913764;JUN:-0.812430834975;VSX1,2:-0.815120173054;HSF1,2:-0.816741560846;ZBTB16:-0.872234538462;PAX8:-0.887228143471;POU3F1..4:-0.895872908792;SMAD1..7,9:-0.905130842987;MZF1:-0.926329521192;FOXL1:-0.930946448095;PRRX1,2:-1.01038017882;KLF4:-1.01076245483;PPARG:-1.01117682953;LEF1_TCF7_TCF7L1,2:-1.01308812469;TFDP1:-1.02216058618;FOX{I1,J2}:-1.04444353175;PBX1:-1.04635755847;CDC5L:-1.05040566635;ADNP_IRX_SIX_ZHX:-1.06913505263;NRF1:-1.10208583036;E2F1..5:-1.11818206934;RFX2..5_RFXANK_RFXAP:-1.11890039793;GATA4:-1.13495474284;NFIX:-1.15688289705;NKX2-2,8:-1.24391574202;BREu{core}:-1.27745065362;POU2F1..3:-1.32236572818;NKX2-1,4:-1.32539131222;SOX2:-1.34856187197;RORA:-1.34966680341;HOX{A4,D4}:-1.36553690944;FOXD3:-1.39417399212;ZNF384:-1.39732703604;NR5A1,2:-1.41673585696;HES1:-1.4283152765;ALX1:-1.48313032952;PRDM1:-1.50566014567;SOX17:-1.51112329862;POU6F1:-1.54037836427;TLX2:-1.55891462922;PAX6:-1.57321141506;NR3C1:-1.5997990172;OCT4_SOX2{dimer}:-1.75297300849;NKX6-1,2:-1.76138586236;SOX{8,9,10}:-1.84367868817;NANOG:-1.84641573223;POU5F1:-1.88817759669;NFY{A,B,C}:-1.89267838715;YY1:-1.96355697646;HOX{A5,B5}:-2.04193470721;GFI1:-2.11241129002;TEF:-2.15866403407;POU1F1:-2.47639836752
|top_motifs=FOXM1:3.26139085194;STAT2,4,6:3.12615293939;FOSL2:3.07917790283;NANOG{mouse}:2.45856337102;FOX{D1,D2}:2.35161948343;RXRA_VDR{dimer}:2.19017474479;BPTF:2.1258536594;AR:2.05922538338;BACH2:1.86344027449;SREBF1,2:1.81840793115;FOS_FOS{B,L1}_JUN{B,D}:1.76820706611;XCPE1{core}:1.66006417954;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.65496408165;SP1:1.61002946614;STAT5{A,B}:1.56896582612;TEAD1:1.55350140877;FOX{F1,F2,J1}:1.44909966945;FOXO1,3,4:1.43998090984;IKZF1:1.34861455648;FOXN1:1.34124412107;TFCP2:1.30083859395;PAX2:1.29196644022;SNAI1..3:1.26830577064;HNF1A:1.24834145914;HNF4A_NR2F1,2:1.24782498961;ZNF148:1.23033625658;HIF1A:1.22898733078;GLI1..3:1.2282593652;EBF1:1.20551802519;GZF1:1.20440574878;NFE2:1.14682803488;TBX4,5:1.04296331687;ZEB1:1.04232493321;PAX1,9:0.958632673023;TP53:0.878946289404;CEBPA,B_DDIT3:0.85882746505;ZNF423:0.852914156971;FOXA2:0.848871611271;MAFB:0.834197322476;ARID5B:0.832448918165;ATF4:0.770072048712;ESR1:0.735305591566;PDX1:0.727822471236;NKX3-2:0.717924879004;NFE2L2:0.710223647645;ATF6:0.647451338211;SPZ1:0.644826944884;MAZ:0.524605021423;PITX1..3:0.497871918084;HLF:0.492708631187;NR1H4:0.425715480645;EN1,2:0.42275975199;HAND1,2:0.412882094616;HMX1:0.39580120738;EP300:0.338644311245;GFI1B:0.303458289885;SRF:0.224052640093;NFKB1_REL_RELA:0.22126900883;EVI1:0.210724459188;ALX4:0.207511630955;TBP:0.176292621242;ETS1,2:0.166807759948;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.162545034462;FOXP1:0.135612971341;ESRRA:0.133796238539;PAX5:0.119941776222;T:0.111895641239;ELK1,4_GABP{A,B1}:0.104500333871;ZIC1..3:0.0988733580815;NR6A1:0.0968171788804;NFE2L1:0.0833859759281;PAX4:0.076398958209;MTE{core}:0.0758758215672;SOX5:0.0739279835355;TFAP2{A,C}:0.0545318101567;STAT1,3:0.0529629266931;ELF1,2,4:0.0431192527781;HMGA1,2:0.0413035080675;IRF1,2:0.0375082538977;MYOD1:0.0272373423745;HOXA9_MEIS1:-0.0131458404838;GCM1,2:-0.0382647603009;RXR{A,B,G}:-0.0439440470419;GTF2I:-0.0760584516978;IKZF2:-0.0772928869952;CREB1:-0.104852092732;EGR1..3:-0.10590608331;TOPORS:-0.111847210426;RREB1:-0.138884646756;ATF2:-0.153155390161;PATZ1:-0.155467459929;SPIB:-0.198353438166;SPI1:-0.200902287523;TLX1..3_NFIC{dimer}:-0.207207355993;FOXQ1:-0.233643342134;DBP:-0.249508923964;AIRE:-0.252127842161;CRX:-0.256680111627;TFAP2B:-0.259734373553;NHLH1,2:-0.275905440298;MYBL2:-0.282316631275;TAL1_TCF{3,4,12}:-0.282615716291;REST:-0.309852750607;TGIF1:-0.309868677434;UFEwm:-0.33518221182;GATA6:-0.354519909419;RBPJ:-0.386041287177;MEF2{A,B,C,D}:-0.391822407381;MYFfamily:-0.409368750679;NFATC1..3:-0.424337139338;ZBTB6:-0.43877103741;NFIL3:-0.453738862673;HBP1_HMGB_SSRP1_UBTF:-0.456418676624;MED-1{core}:-0.469379976592;ATF5_CREB3:-0.499740536008;TFAP4:-0.502851669051;NKX2-3_NKX2-5:-0.526815378381;HIC1:-0.533070663224;FOXP3:-0.539584414591;DMAP1_NCOR{1,2}_SMARC:-0.543468450547;NKX3-1:-0.561232811429;CDX1,2,4:-0.580052456661;ZNF238:-0.591794851959;bHLH_family:-0.653973085355;LHX3,4:-0.661414330967;IRF7:-0.678302403169;MYB:-0.691356959269;ZNF143:-0.693627295401;ZFP161:-0.705224321805;CUX2:-0.707460210039;AHR_ARNT_ARNT2:-0.722505150136;RUNX1..3:-0.75925870364;ONECUT1,2:-0.770828497778;LMO2:-0.777117516479;RFX1:-0.778801272361;GTF2A1,2:-0.780249520574;MTF1:-0.784068913764;JUN:-0.812430834975;VSX1,2:-0.815120173054;HSF1,2:-0.816741560846;ZBTB16:-0.872234538462;PAX8:-0.887228143471;POU3F1..4:-0.895872908792;SMAD1..7,9:-0.905130842987;MZF1:-0.926329521192;FOXL1:-0.930946448095;PRRX1,2:-1.01038017882;KLF4:-1.01076245483;PPARG:-1.01117682953;LEF1_TCF7_TCF7L1,2:-1.01308812469;TFDP1:-1.02216058618;FOX{I1,J2}:-1.04444353175;PBX1:-1.04635755847;CDC5L:-1.05040566635;ADNP_IRX_SIX_ZHX:-1.06913505263;NRF1:-1.10208583036;E2F1..5:-1.11818206934;RFX2..5_RFXANK_RFXAP:-1.11890039793;GATA4:-1.13495474284;NFIX:-1.15688289705;NKX2-2,8:-1.24391574202;BREu{core}:-1.27745065362;POU2F1..3:-1.32236572818;NKX2-1,4:-1.32539131222;SOX2:-1.34856187197;RORA:-1.34966680341;HOX{A4,D4}:-1.36553690944;FOXD3:-1.39417399212;ZNF384:-1.39732703604;NR5A1,2:-1.41673585696;HES1:-1.4283152765;ALX1:-1.48313032952;PRDM1:-1.50566014567;SOX17:-1.51112329862;POU6F1:-1.54037836427;TLX2:-1.55891462922;PAX6:-1.57321141506;NR3C1:-1.5997990172;OCT4_SOX2{dimer}:-1.75297300849;NKX6-1,2:-1.76138586236;SOX{8,9,10}:-1.84367868817;NANOG:-1.84641573223;POU5F1:-1.88817759669;NFY{A,B,C}:-1.89267838715;YY1:-1.96355697646;HOX{A5,B5}:-2.04193470721;GFI1:-2.11241129002;TEF:-2.15866403407;POU1F1:-2.47639836752
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:583-22A8;search_select_hide=table117:583-22A8
}}
}}

Latest revision as of 19:18, 4 June 2020


Name:amnion, adult pregnant day17.5
Species:Mouse (Mus musculus)
Library ID:CNhs10488
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissueamnion
dev stage17.5 days pregnant adult
sexfemale
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004853
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10488 CAGE DRX008934 DRR009808
Accession ID Mm9

Library idBAMCTSS
CNhs10488 DRZ001233 DRZ002616
Accession ID Mm10

Library idBAMCTSS
CNhs10488 DRZ012583 DRZ013966
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs10488



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: CNhs10488



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: CNhs10488



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: CNhs10488


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
0000468 (multi-cellular organism)
0007023 (adult organism)
0000305 (amnion)
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)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000317 (mouse pregnant tissue sample)
0000322 (mouse pregnant day 17.5 sample)
0011386 (mouse amnion - adult pregnant day17.5 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
UBERON:0004871 (somatic layer of lateral plate mesoderm)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)