FF:10618-108G6: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |F5samples= | ||
| | |ancestors_in_anatomy_facet= | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
| | |comment= | ||
|created_by= | |||
|creation_date= | |||
|def= | |||
|fonse_cell_line=FF:0101575 | |fonse_cell_line=FF:0101575 | ||
|fonse_cell_line_closure=FF:0101575 | |fonse_cell_line_closure=FF:0101575 | ||
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|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|id=FF:10618-108G6 | |||
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0101575 | |is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0101575 | ||
|name=choriocarcinoma cell line:T3M-3 | |||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan=,,, | |||
|profile_hcage=CNhs11820,LSID829,release010,COMPLETED | |||
|profile_rnaseq=,,, | |||
|profile_srnaseq=,,, | |||
|rna_box=108 | |||
|rna_catalog_number= | |||
|rna_concentration=2.4172 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |||
|rna_lot_number= | |||
|rna_od260/230=2.12 | |||
|rna_od260/280=2.04 | |||
|rna_position=G6 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=108G6 | |||
|rna_weight_ug=181.29 | |||
|sample_age=fetal | |||
|sample_cell_catalog=RCB1018 | |||
|sample_cell_line=T3M-3 | |||
|sample_cell_lot= | |||
|sample_cell_type=trophoblast cell | |||
|sample_collaboration=Yukio Nakamura (RIKEN BRC) | |||
|sample_company=RIKEN Bioresource centre | |||
|sample_description= | |||
|sample_dev_stage= | |||
|sample_disease=choriocarcinoma | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity=J | |||
|sample_experimental_condition= | |||
|sample_id=10618 | |||
|sample_note= | |||
|sample_sex=unknown | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=chorioamniotic membrane | |||
|top_motifs=VSX1,2:2.23307754789;SNAI1..3:1.56633807648;HOXA9_MEIS1:1.4061433732;RORA:1.39103643952;PITX1..3:1.27644048852;PAX1,9:1.22000757533;ESRRA:1.21921406967;ZEB1:1.19721557635;MYOD1:1.17391624087;HOX{A6,A7,B6,B7}:1.1626361047;bHLH_family:1.12117607961;FOXP1:1.05480939124;FOXD3:1.04986826276;ELK1,4_GABP{A,B1}:1.01691276425;HOX{A5,B5}:0.991283269922;TEAD1:0.945380708158;FOXQ1:0.846904527752;XCPE1{core}:0.815137264543;SP1:0.734982431243;LMO2:0.714978039976;NFY{A,B,C}:0.710707273501;CDC5L:0.659842806402;GATA6:0.619743470237;OCT4_SOX2{dimer}:0.611147501923;FOXN1:0.608183884622;TOPORS:0.593853851666;ZNF384:0.531194489597;RBPJ:0.512898947138;HLF:0.512648732815;ZNF143:0.495998119232;HIF1A:0.473482997057;E2F1..5:0.469193622588;NKX3-2:0.459150558942;NRF1:0.436142399324;POU1F1:0.433942465902;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.428494449728;PRRX1,2:0.421305851503;CUX2:0.406110578065;POU2F1..3:0.381747034497;FOX{F1,F2,J1}:0.370528032615;FOXA2:0.357673066999;BREu{core}:0.353517418122;ALX1:0.344272571074;AIRE:0.337100672604;LHX3,4:0.336167847868;GFI1:0.324296593296;SREBF1,2:0.317666045391;TEF:0.257471704476;CEBPA,B_DDIT3:0.252786315649;SOX17:0.217514096765;LEF1_TCF7_TCF7L1,2:0.189510261167;MYB:0.188694293108;PAX4:0.159036470206;STAT5{A,B}:0.137557331954;ADNP_IRX_SIX_ZHX:0.129129822223;HNF1A:0.112471154337;PBX1:0.107215398337;NFIX:0.0727034884098;ZFP161:0.0719397354401;HNF4A_NR2F1,2:0.0402222465827;TFDP1:0.0354004915336;MED-1{core}:0.024679020233;CRX:0.0137058893087;FOX{I1,J2}:0.00186775140456;EVI1:-0.0100560285006;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.0115182627335;YY1:-0.0128849095417;TP53:-0.0147089097407;KLF4:-0.0190960789644;FOXL1:-0.0353646021572;PAX2:-0.036092693403;IKZF1:-0.0462838961689;MYBL2:-0.0474575083855;HOX{A4,D4}:-0.0521869549708;POU6F1:-0.0644032318247;PDX1:-0.0795948795333;ONECUT1,2:-0.079944171799;SOX5:-0.081727704697;NFE2L2:-0.125293664673;NANOG:-0.168832086023;PATZ1:-0.168988653588;ESR1:-0.171760025514;ELF1,2,4:-0.18468212615;PAX3,7:-0.188230214857;IKZF2:-0.193303703673;SOX{8,9,10}:-0.214453562008;TBX4,5:-0.220889493759;ZBTB16:-0.226609990225;ZNF423:-0.250272596867;TFAP2B:-0.259089766422;RFX2..5_RFXANK_RFXAP:-0.298189502713;ZIC1..3:-0.304355670421;ARID5B:-0.310537052761;CREB1:-0.31268283381;EN1,2:-0.314347707748;ALX4:-0.324323596005;GATA4:-0.343343644407;NR5A1,2:-0.343662141152;TFAP2{A,C}:-0.347266751297;FOS_FOS{B,L1}_JUN{B,D}:-0.35182623293;SOX2:-0.360130757254;CDX1,2,4:-0.370478927422;MTF1:-0.376331995192;STAT2,4,6:-0.385469185579;NFE2:-0.401191339534;ZNF238:-0.413252293677;XBP1:-0.418210400069;BACH2:-0.424920385528;EGR1..3:-0.427795874909;NKX2-3_NKX2-5:-0.435042781205;EBF1:-0.457085004207;ATF4:-0.472091271433;MEF2{A,B,C,D}:-0.479766882534;ATF2:-0.483337831345;NFKB1_REL_RELA:-0.501712454803;SPIB:-0.513832901274;AHR_ARNT_ARNT2:-0.536469161984;DMAP1_NCOR{1,2}_SMARC:-0.537356642518;RUNX1..3:-0.545664619454;FOSL2:-0.550032985257;RFX1:-0.566668814518;FOXO1,3,4:-0.56880281698;STAT1,3:-0.583632413149;GCM1,2:-0.588992650124;SPI1:-0.590924116669;ZNF148:-0.592484420862;ETS1,2:-0.600526156286;TAL1_TCF{3,4,12}:-0.60128056609;ATF5_CREB3:-0.603925179831;DBP:-0.613781996138;HMGA1,2:-0.617369402191;FOXP3:-0.618812603457;NKX2-1,4:-0.622953322014;NKX2-2,8:-0.628497377422;NR1H4:-0.650602654264;UFEwm:-0.65239663206;FOXM1:-0.670976397548;NFIL3:-0.672565942749;ZBTB6:-0.674433131678;TGIF1:-0.704790017588;HES1:-0.706934659302;GTF2I:-0.707571498749;SPZ1:-0.713571880208;PAX8:-0.714120856378;HIC1:-0.726879040025;GFI1B:-0.741352362366;BPTF:-0.756040500715;PAX6:-0.768505417932;FOX{D1,D2}:-0.76853058416;MAFB:-0.768598683742;NFE2L1:-0.774980633645;MYFfamily:-0.793519530897;GTF2A1,2:-0.793798478688;MAZ:-0.796013348502;POU5F1:-0.797468508066;PAX5:-0.835949033254;JUN:-0.847904985538;NKX6-1,2:-0.850814596657;TLX1..3_NFIC{dimer}:-0.857765794073;TFAP4:-0.864366464577;HAND1,2:-0.886363092492;NR3C1:-0.892767888309;GZF1:-0.91220078359;REST:-0.951416050006;POU3F1..4:-0.966639068891;HMX1:-0.970020838544;NHLH1,2:-0.971601842836;AR:-1.02546253325;RREB1:-1.03736462965;ATF6:-1.05855520736;T:-1.0633470261;TBP:-1.10131626602;MTE{core}:-1.12426169466;IRF7:-1.12833091923;PRDM1:-1.15357501854;HBP1_HMGB_SSRP1_UBTF:-1.17546522142;NKX3-1:-1.19084514848;SRF:-1.19319707634;NFATC1..3:-1.24200685134;TLX2:-1.24576720578;MZF1:-1.24576825868;TFCP2:-1.31471380291;HSF1,2:-1.33967612609;RXRA_VDR{dimer}:-1.34213215097;PPARG:-1.3546437829;NR6A1:-1.41206837723;NANOG{mouse}:-1.43452395806;GLI1..3:-1.52602417886;IRF1,2:-1.55080468711;EP300:-1.57292862467;RXR{A,B,G}:-1.61041433671;SMAD1..7,9:-2.01300367262 | |||
}} | }} |
Revision as of 14:11, 21 March 2012
Name: | choriocarcinoma cell line:T3M-3 |
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Species: | Human (Homo sapiens) |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
Additional information | ||||||||||||||||||||||||||||
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Sample information
RNA information
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Download raw sequence, BAM & CTSS | ||||||||||||
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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: CNhs11820
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: CNhs11820
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: CNhs11820
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
FF:0101575 choriocarcinoma cell line 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
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