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{{f5samples
{{f5samples
|id=FF:1985-43F5
|ancestors_in_anatomy_facet=UBERON:0000026,UBERON:0000061,UBERON:0000062,UBERON:0000075,UBERON:0000154,UBERON:0000376,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000978,UBERON:0000981,UBERON:0001048,UBERON:0001062,UBERON:0001271,UBERON:0001434,UBERON:0001464,UBERON:0001474,UBERON:0002050,UBERON:0002091,UBERON:0002101,UBERON:0002103,UBERON:0002204,UBERON:0002428,UBERON:0002472,UBERON:0002495,UBERON:0002529,UBERON:0002532,UBERON:0003081,UBERON:0003102,UBERON:0003464,UBERON:0003606,UBERON:0003608,UBERON:0003826,UBERON:0004120,UBERON:0004347,UBERON:0004357,UBERON:0004375,UBERON:0004708,UBERON:0004709,UBERON:0004765,UBERON:0005423,UBERON:0005732,UBERON:0005733,UBERON:0006057,UBERON:0006058,UBERON:0007823,UBERON:0007828,UBERON:0008202,UBERON:0008784
|name=bone (os femoris), neonate N02
|sample_id=1985
|rna_tube_id=43F5
|rna_box=43
|rna_position=F5
|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=2 days neonate
|sample_tissue=bone (os femoris)
|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=CNhs11227,LSID748,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000026,UBERON:0000061,UBERON:0000062,UBERON:0000075,UBERON:0000154,UBERON:0000376,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000978,UBERON:0000981,UBERON:0001048,UBERON:0001062,UBERON:0001271,UBERON:0001434,UBERON:0001464,UBERON:0001474,UBERON:0002050,UBERON:0002091,UBERON:0002101,UBERON:0002103,UBERON:0002204,UBERON:0002428,UBERON:0002472,UBERON:0002495,UBERON:0002529,UBERON:0002532,UBERON:0003081,UBERON:0003102,UBERON:0003464,UBERON:0003606,UBERON:0003608,UBERON:0003826,UBERON:0004120,UBERON:0004347,UBERON:0004357,UBERON:0004375,UBERON:0004708,UBERON:0004709,UBERON:0004765,UBERON:0005423,UBERON:0005732,UBERON:0005733,UBERON:0006057,UBERON:0006058,UBERON:0007823,UBERON:0007828,UBERON:0008202,UBERON:0008784
|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=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:1985-43F5
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011463
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011463
|name=bone (os femoris), neonate N02
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11227,LSID748,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=43
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=F5
|rna_rin=
|rna_sample_type=
|rna_tube_id=43F5
|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=2 days neonate
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=1985
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=bone (os femoris)
|top_motifs=MEF2{A,B,C,D}:2.78240229567;FOXL1:2.63101679178;ESR1:2.04445864671;NKX2-3_NKX2-5:2.0352020107;TFAP4:1.93207883782;TAL1_TCF{3,4,12}:1.91678328147;ZNF238:1.7532706917;GCM1,2:1.72623498929;TOPORS:1.54364766062;IKZF2:1.44534255941;NFATC1..3:1.38924611137;HES1:1.37647598257;SOX5:1.36551272245;RXR{A,B,G}:1.34227472304;TEAD1:1.32261441343;MYBL2:1.3151328993;TLX2:1.31371214328;GLI1..3:1.29970120844;SRF:1.24735150906;TGIF1:1.24185256484;GATA4:1.22269895702;ALX1:1.21015914848;FOXP3:1.20025071525;TFCP2:1.18928797906;HOX{A4,D4}:1.18039910234;EVI1:1.15012352961;IKZF1:1.1032490843;SMAD1..7,9:1.08258100624;TFAP2{A,C}:1.08086345308;NFE2L2:1.04748458009;PAX1,9:1.04684087378;HIF1A:0.98973358323;GFI1:0.969007791671;EP300:0.965209284578;TLX1..3_NFIC{dimer}:0.93913041053;HMGA1,2:0.924595318156;PRDM1:0.914549750377;KLF4:0.889250138154;ZNF423:0.878438281506;MAZ:0.831574553685;IRF7:0.823215013728;HSF1,2:0.817046383436;NR1H4:0.813669644959;UFEwm:0.802831565068;MYOD1:0.768791239886;MTF1:0.745234927246;MAFB:0.739266121849;NR3C1:0.729886326859;NR6A1:0.725004783296;ZNF148:0.700068507341;ATF6:0.673461973655;RREB1:0.66447303197;TFAP2B:0.658952833872;PAX2:0.633273729327;NHLH1,2:0.619606316749;RXRA_VDR{dimer}:0.615280251361;TBP:0.60254310507;NKX2-1,4:0.574222131181;GFI1B:0.569829534152;PATZ1:0.569031089261;HIC1:0.549866888591;CRX:0.549324760471;SPIB:0.508759091161;EBF1:0.492610128212;GATA6:0.488674569996;ZNF384:0.479141835681;SPZ1:0.470021862049;MYFfamily:0.469747259906;SOX{8,9,10}:0.461551339677;MZF1:0.451296666349;STAT2,4,6:0.444800535326;MTE{core}:0.439309535625;E2F1..5:0.436122307504;DMAP1_NCOR{1,2}_SMARC:0.41190495085;ALX4:0.40616728891;NANOG{mouse}:0.379710936797;HOX{A5,B5}:0.365980713896;PITX1..3:0.350041890211;PAX5:0.316741037285;GTF2I:0.310490999047;ZIC1..3:0.30327129565;SPI1:0.302493803878;RUNX1..3:0.299654052962;SP1:0.279749434841;STAT5{A,B}:0.264535769375;XCPE1{core}:0.264375338398;FOXO1,3,4:0.258794162277;FOSL2:0.245179905451;NR5A1,2:0.243662014372;NFE2L1:0.221096195387;FOXP1:0.209358219688;PAX4:0.204648338591;POU5F1:0.19990965103;GTF2A1,2:0.198829220622;CDC5L:0.151016378367;AR:0.107480090369;FOS_FOS{B,L1}_JUN{B,D}:0.0912003061518;TP53:0.0815921290055;EGR1..3:0.058161999908;CUX2:0.048087674505;NFE2:0.0317459350975;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.0292684661354;HMX1:0.0232980451596;TEF:0.019604733537;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.00367349083049;ZNF143:-0.0151498230891;NKX2-2,8:-0.0276356601503;SREBF1,2:-0.0349061891302;TFDP1:-0.0362028331952;PPARG:-0.0479862587518;NFKB1_REL_RELA:-0.0490323827895;BPTF:-0.0521150228437;BACH2:-0.0616885504386;YY1:-0.0626434662804;ELF1,2,4:-0.0991126919386;ETS1,2:-0.102548437804;ARID5B:-0.117153559468;LMO2:-0.13199539605;SOX17:-0.142144382364;AIRE:-0.145710798788;FOX{I1,J2}:-0.148864418813;BREu{core}:-0.160021242437;TBX4,5:-0.176712898093;POU1F1:-0.191445689509;ZFP161:-0.192630792116;HBP1_HMGB_SSRP1_UBTF:-0.197865427263;MYB:-0.201476395053;MED-1{core}:-0.216926536332;RFX2..5_RFXANK_RFXAP:-0.226217919514;RORA:-0.241894516728;FOXA2:-0.245153105012;HOXA9_MEIS1:-0.254115057208;CDX1,2,4:-0.259591411646;IRF1,2:-0.277693157981;ESRRA:-0.294875583919;POU3F1..4:-0.298253302866;PDX1:-0.303251669045;HLF:-0.328329630778;POU6F1:-0.391401813815;ATF4:-0.403038599122;ATF2:-0.436494719138;RBPJ:-0.439338285256;REST:-0.464797219498;SOX2:-0.479349032135;CEBPA,B_DDIT3:-0.494889036144;LHX3,4:-0.49734768617;CREB1:-0.502932088004;PAX6:-0.52247064938;JUN:-0.540287194429;NRF1:-0.548201982818;ZBTB16:-0.554882368498;AHR_ARNT_ARNT2:-0.589630275586;FOX{F1,F2,J1}:-0.596302182938;DBP:-0.605645505577;RFX1:-0.621395128698;PRRX1,2:-0.624285756876;HAND1,2:-0.628643777598;HNF4A_NR2F1,2:-0.631614999087;ATF5_CREB3:-0.647689302056;NKX6-1,2:-0.653579117474;EN1,2:-0.656141838038;T:-0.678467885691;NKX3-1:-0.711868700555;VSX1,2:-0.736397094378;HNF1A:-0.762920330223;NKX3-2:-0.778658829332;NFY{A,B,C}:-0.784800276247;PBX1:-0.8069051827;FOXN1:-0.854114023621;OCT4_SOX2{dimer}:-0.866931617574;FOX{D1,D2}:-0.874191316289;POU2F1..3:-0.884077748769;PAX8:-0.897342287722;LEF1_TCF7_TCF7L1,2:-0.9122790854;ZBTB6:-0.912682547671;ELK1,4_GABP{A,B1}:-0.97573926844;GZF1:-1.05799266506;FOXD3:-1.12023780042;NFIX:-1.12280102916;SNAI1..3:-1.13148534673;NFIL3:-1.26971790536;NANOG:-1.28822966788;FOXQ1:-1.30238746717;ADNP_IRX_SIX_ZHX:-1.40983154826;ZEB1:-1.45523372534;STAT1,3:-1.60031333743;bHLH_family:-1.7843022316;FOXM1:-1.85885195512;ONECUT1,2:-1.93549463189
}}
}}

Revision as of 15:33, 21 March 2012


Name:bone (os femoris), neonate N02
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuebone (os femoris)
dev stage2 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
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
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

CNhs11227

00
10
100
1000
10000.354
10010.348
10020.0712
10030.283
10040
10050.144
10060.454
10070.0472
10080
10090.237
1010.00728
10100
1011-0.026
10120
1013-0.0774
10140.462
10152.684411e-4
10160.209
10170
10180
10190
1020
10200
10210.0164
10220.418
10230
10240.274
10250
10260.0651
10270.239
10280
10290.262
1030.957
10300.0651
10310.262
10320.137
1033-0.0419
10340
10350.0977
1036-0.0113
10370
10380.111
10390.067
1040
10400.232
10410.0651



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: CNhs11227

Jaspar motifP-value
MA0002.20.64
MA0003.10.0471
MA0004.10.0879
MA0006.10.0795
MA0007.10.894
MA0009.10.255
MA0014.10.408
MA0017.10.00612
MA0018.21.48201e-4
MA0019.10.112
MA0024.10.856
MA0025.10.0271
MA0027.10.0621
MA0028.13.10538e-6
MA0029.10.284
MA0030.10.433
MA0031.10.139
MA0035.20.568
MA0038.10.996
MA0039.20.477
MA0040.10.169
MA0041.10.102
MA0042.10.76
MA0043.10.0148
MA0046.13.04597e-16
MA0047.20.0168
MA0048.10.343
MA0050.10.0181
MA0051.10.0538
MA0052.17.64668e-36
MA0055.10.0181
MA0057.10.41
MA0058.10.114
MA0059.10.0843
MA0060.10.0109
MA0061.10.338
MA0062.28.54191e-11
MA0065.20.903
MA0066.10.899
MA0067.10.0129
MA0068.10.0402
MA0069.10.107
MA0070.10.812
MA0071.10.224
MA0072.10.132
MA0073.10.824
MA0074.10.811
MA0076.13.56e-7
MA0077.10.295
MA0078.10.175
MA0079.20.0577
MA0080.20.0713
MA0081.10.823
MA0083.14.62437e-8
MA0084.10.818
MA0087.10.644
MA0088.10.383
MA0090.10.0745
MA0091.10.0354
MA0092.10.231
MA0093.10.147
MA0099.20.61
MA0100.10.0744
MA0101.10.557
MA0102.20.654
MA0103.11.58556e-6
MA0104.20.0481
MA0105.10.505
MA0106.10.886
MA0107.10.84
MA0108.21.75486e-5
MA0111.10.958
MA0112.20.00476
MA0113.10.707
MA0114.10.00213
MA0115.10.101
MA0116.10.54
MA0117.10.701
MA0119.10.41
MA0122.10.858
MA0124.10.937
MA0125.10.669
MA0131.10.464
MA0135.10.934
MA0136.10.00125
MA0137.20.00125
MA0138.20.771
MA0139.10.0472
MA0140.10.0138
MA0141.10.872
MA0142.10.215
MA0143.10.851
MA0144.10.112
MA0145.10.107
MA0146.10.415
MA0147.10.134
MA0148.10.0415
MA0149.10.0423
MA0150.10.259
MA0152.10.0678
MA0153.11.51683e-13
MA0154.10.0893
MA0155.10.0795
MA0156.19.54522e-5
MA0157.10.519
MA0159.10.727
MA0160.10.439
MA0162.10.269
MA0163.10.124
MA0164.10.537
MA0258.10.219
MA0259.10.366



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: CNhs11227

Novel motifP-value
10.828
100.717
1000.731
1010.693
1020.781
1030.313
1040.778
1050.103
1060.14
1070.0862
1080.699
1090.234
110.876
1100.621
1110.778
1120.444
1130.976
1140.826
1151
1160.473
1170.614
1180.888
1190.685
120.123
1200.259
1210.683
1220.864
1230.953
1240.0785
1250.38
1260.782
1270.174
1280.492
1290.717
130.0845
1300.857
1310.771
1320.798
1330.647
1340.857
1350.678
1360.36
1370.325
1380.167
1390.946
140.695
1400.239
1410.944
1420.487
1430.996
1440.00131
1450.614
1460.543
1470.772
1480.819
1490.869
150.213
1500.208
1510.756
1520.027
1530.236
1540.624
1550.946
1566.70933e-17
1570.704
1580.858
1590.104
1600.0584
1610.208
1620.582
1630.465
1640.605
1650.822
1660.276
1670.314
1680.132
1690.00227
170.586
180.445
190.0302
20.227
200.785
210.999
220.177
230.656
240.514
250.597
260.0419
270.648
280.302
290.331
30.96
300.634
310.913
320.00912
330.32
340.0689
350.0427
360.0727
370.211
380.419
390.245
40.977
400.0725
410.292
420.691
430.567
440.167
450.237
460.381
470.669
480.533
490.677
50.075
500.0477
510.989
520.174
530.671
540.523
550.997
560.71
570.89
580.805
590.0132
60.318
600.158
610.97
620.912
630.21
640.566
650.377
660.701
670.224
680.449
690.39
70.277
700.515
710.19
720.307
730.139
740.988
750.378
760.615
770.356
780.0379
790.444
80.903
800.642
810.563
820.961
830.772
840.809
850.103
860.971
870.0168
880.711
890.264
90.182
900.0403
910.0209
920.392
930.108
940.569
950.305
960.488
970.443
980.563
990.59



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: CNhs11227


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
0000026 (appendage)
0000061 (anatomical structure)
0000062 (organ)
0000075 (subdivision of skeletal system)
0000154 (posterior region of body)
0000376 (hindlimb stylopod)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000978 (leg)
0000981 (femur)
0001048 (primordium)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002091 (appendicular skeleton)
0002101 (limb)
0002103 (hindlimb)
0002204 (musculoskeletal system)
0002428 (limb bone)
0002472 (stylopod)
0002495 (long bone)
0002529 (limb segment)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003102 (surface structure)
0003464 (hindlimb bone)
0003606 (limb long bone)
0003608 (hindlimb long bone)
0003826 (upper leg bone)
0004120 (mesoderm-derived structure)
0004347 (limb bud)
0004357 (paired limb/fin bud)
0004375 (bone of free limb or fin)
0004708 (paired limb/fin)
0004709 (pelvic appendage)
0004765 (skeletal element)
0005423 (developing anatomical structure)
0005732 (limb/fin field)
0005733 (limb field)
0006058 (multi-limb segment region)
0008202 (bone of hip region)
0008784 (lower limb segment)

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

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