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{{f5samples
{{f5samples
|id=FF:2104-43C7
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000065,UBERON:0000072,UBERON:0000077,UBERON:0000078,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000490,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0000974,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001042,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0001557,UBERON:0002050,UBERON:0002193,UBERON:0002342,UBERON:0002346,UBERON:0002368,UBERON:0002370,UBERON:0002390,UBERON:0002405,UBERON:0002530,UBERON:0002532,UBERON:0003075,UBERON:0003104,UBERON:0003295,UBERON:0003351,UBERON:0003408,UBERON:0003929,UBERON:0004119,UBERON:0004120,UBERON:0004121,UBERON:0004177,UBERON:0004185,UBERON:0004807,UBERON:0004921,UBERON:0005057,UBERON:0005058,UBERON:0005291,UBERON:0005423,UBERON:0005428,UBERON:0005434,UBERON:0005562,UBERON:0005911,UBERON:0006562,UBERON:0006598,UBERON:0007026,UBERON:0007284,UBERON:0007690,UBERON:0009113,UBERON:0009142,UBERON:0009145
|name=thymus, neonate N03
|sample_id=2104
|rna_tube_id=43C7
|rna_box=43
|rna_position=C7
|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=3 days neonate
|sample_tissue=thymus
|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=CNhs11137,LSID735,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:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000065,UBERON:0000072,UBERON:0000077,UBERON:0000078,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000490,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0000974,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001042,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0001557,UBERON:0002050,UBERON:0002193,UBERON:0002342,UBERON:0002346,UBERON:0002368,UBERON:0002370,UBERON:0002390,UBERON:0002405,UBERON:0002530,UBERON:0002532,UBERON:0003075,UBERON:0003104,UBERON:0003295,UBERON:0003351,UBERON:0003408,UBERON:0003929,UBERON:0004119,UBERON:0004120,UBERON:0004121,UBERON:0004177,UBERON:0004185,UBERON:0004807,UBERON:0004921,UBERON:0005057,UBERON:0005058,UBERON:0005291,UBERON:0005423,UBERON:0005428,UBERON:0005434,UBERON:0005562,UBERON:0005911,UBERON:0006562,UBERON:0006598,UBERON:0007026,UBERON:0007284,UBERON:0007690,UBERON:0009113,UBERON:0009142,UBERON:0009145
|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:2104-43C7
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011304
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011304
|name=thymus, neonate N03
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11137,LSID735,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=C7
|rna_rin=
|rna_sample_type=
|rna_tube_id=43C7
|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=3 days neonate
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=2104
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=thymus
|top_motifs=PITX1..3:2.44928602258;RORA:2.28540772304;ALX4:2.26521359701;TEF:2.23176528515;E2F1..5:2.04704843476;ZBTB16:1.85900072825;ELF1,2,4:1.817132296;PPARG:1.77776231749;ETS1,2:1.71525007107;SPZ1:1.69363262134;RUNX1..3:1.69050299822;FOXP1:1.67535603983;AIRE:1.54304046569;TLX2:1.52791551492;DMAP1_NCOR{1,2}_SMARC:1.51181197941;CDX1,2,4:1.50468262215;POU1F1:1.47612185895;SPI1:1.45207819267;IRF1,2:1.34060849358;NFY{A,B,C}:1.21843060039;SPIB:1.19100449959;NFKB1_REL_RELA:1.03892988099;MYB:1.0118460205;FOXD3:0.977980960227;ELK1,4_GABP{A,B1}:0.952214374938;FOXP3:0.937825182004;EN1,2:0.931254043833;NFATC1..3:0.92484044159;PAX4:0.751045933481;POU5F1:0.674051901412;LMO2:0.657174745873;BPTF:0.652152113459;GFI1:0.649061770814;IRF7:0.558215465424;STAT1,3:0.53872257444;PDX1:0.510830014082;RXRA_VDR{dimer}:0.48483356297;SNAI1..3:0.433202757882;NR6A1:0.431269077254;NRF1:0.387423092158;ZEB1:0.385643606321;YY1:0.335529426399;ZNF384:0.314516836874;SOX{8,9,10}:0.303487316249;ZNF143:0.255666627049;NFIX:0.231481724575;TAL1_TCF{3,4,12}:0.194126608114;NANOG{mouse}:0.19106415667;LEF1_TCF7_TCF7L1,2:0.18077612694;ZNF238:0.178827522822;PBX1:0.173247161212;STAT5{A,B}:0.121916721803;TFDP1:0.114426185429;IKZF2:0.106340470305;TOPORS:0.0889359529953;RBPJ:0.0615752765549;OCT4_SOX2{dimer}:0.0414229900277;HOX{A4,D4}:-0.0272218513902;FOX{I1,J2}:-0.0283016437774;SOX2:-0.0403766496066;NKX6-1,2:-0.0410026308509;NR1H4:-0.0726690275357;POU2F1..3:-0.0756335754851;HLF:-0.0801536411276;CRX:-0.0802882585475;SOX17:-0.104331823176;FOXO1,3,4:-0.119911962095;TBP:-0.120218677849;NANOG:-0.135860046594;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.144379402981;HES1:-0.144450558842;FOXM1:-0.153207111685;PRDM1:-0.156495289596;MYOD1:-0.163694687268;KLF4:-0.164753218225;HOX{A5,B5}:-0.171250945688;ATF5_CREB3:-0.189896590428;RREB1:-0.195715557743;SREBF1,2:-0.204106401555;NKX2-1,4:-0.212801518495;BREu{core}:-0.221837569121;CEBPA,B_DDIT3:-0.239415899357;RFX2..5_RFXANK_RFXAP:-0.243399737805;ALX1:-0.249972619479;CUX2:-0.263276606318;NHLH1,2:-0.282833997604;PAX8:-0.289641969031;FOXL1:-0.307677799429;HBP1_HMGB_SSRP1_UBTF:-0.32791804221;PAX6:-0.333854487293;SRF:-0.343789042257;NKX2-2,8:-0.34401843475;NFE2L1:-0.354189945562;GATA6:-0.359563469987;CDC5L:-0.371586487893;FOXQ1:-0.373575867623;TGIF1:-0.381335241609;FOS_FOS{B,L1}_JUN{B,D}:-0.381937743064;POU6F1:-0.385753548104;T:-0.393424811487;ARID5B:-0.394614342459;TBX4,5:-0.424811178824;POU3F1..4:-0.435671718094;FOX{D1,D2}:-0.46226972077;PRRX1,2:-0.475457598087;MTE{core}:-0.483755808322;EBF1:-0.493770518278;ZFP161:-0.502221553901;MZF1:-0.502340603023;SMAD1..7,9:-0.528722472082;JUN:-0.55358754815;ESR1:-0.554785758308;HNF4A_NR2F1,2:-0.565811715837;MEF2{A,B,C,D}:-0.566782534167;HMX1:-0.574132910931;NR5A1,2:-0.594046586315;NKX2-3_NKX2-5:-0.60803748987;RXR{A,B,G}:-0.629188049953;TP53:-0.6315692978;EVI1:-0.647823153659;NKX3-1:-0.649880202465;AR:-0.652054108502;MYFfamily:-0.653471688626;BACH2:-0.656068412789;AHR_ARNT_ARNT2:-0.665562959015;MYBL2:-0.669500640546;ZNF423:-0.70573738373;PATZ1:-0.708998659574;ZNF148:-0.721649358112;RFX1:-0.729301319322;HNF1A:-0.749641694366;MTF1:-0.749825421875;UFEwm:-0.751673299176;EP300:-0.763629021013;GATA4:-0.772951920222;FOX{F1,F2,J1}:-0.778274656741;LHX3,4:-0.790209847676;STAT2,4,6:-0.794431922257;NR3C1:-0.79864893316;CREB1:-0.818881673506;HMGA1,2:-0.830968318602;NFE2:-0.883143378875;FOXA2:-0.894834651868;MED-1{core}:-0.896452781868;DBP:-0.913532892336;VSX1,2:-0.916885445966;bHLH_family:-0.929239776642;PAX2:-0.977682826758;HSF1,2:-0.994881800954;TEAD1:-1.00292716579;SOX5:-1.01434417495;REST:-1.01646643226;EGR1..3:-1.01873969282;HIC1:-1.03421651502;FOXN1:-1.07261969544;GTF2I:-1.08590945969;HAND1,2:-1.08714631265;ATF4:-1.10879234426;FOSL2:-1.11428128743;XCPE1{core}:-1.12496044749;TFAP4:-1.13375524232;TFAP2B:-1.14616447262;MAZ:-1.15875937847;NFIL3:-1.16978429199;MAFB:-1.18230303069;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.19126691397;ESRRA:-1.20060571261;ONECUT1,2:-1.20542556997;ATF2:-1.21705836808;NKX3-2:-1.22819861696;NFE2L2:-1.25096629195;ZIC1..3:-1.25251695296;TFCP2:-1.25647329369;TLX1..3_NFIC{dimer}:-1.26102265331;PAX1,9:-1.26183835701;HOXA9_MEIS1:-1.30315680583;GZF1:-1.33732781315;ZBTB6:-1.34180971264;TFAP2{A,C}:-1.43192942576;GCM1,2:-1.58018149575;IKZF1:-1.58509388069;SP1:-1.59923483325;ATF6:-1.6523160401;ADNP_IRX_SIX_ZHX:-1.6586099854;GFI1B:-1.70805856683;GTF2A1,2:-1.79273074712;GLI1..3:-1.86379165986;PAX5:-2.18211118642;HIF1A:-2.71051908211
}}
}}

Revision as of 15:33, 21 March 2012


Name:thymus, neonate N03
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuethymus
dev stage3 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

CNhs11137

00
10
100
1000
1000-0.0154
10010.0201
10020.0354
1003-0.0553
10040
10050
1006-0.0828
10070.06
10080
1009-0.13
1010.144
10100
10110
10120.345
1013-0.153
1014-0.0851
10150.0974
1016-0.267
10170
10180.0598
10190
1020.0598
10200
10210
1022-0.173
10230
1024-0.0899
1025-0.0611
10260
1027-0.048
10280
10290.295
103-0.025
10300
1031-0.473
1032-0.341
1033-0.00432
10340
10350
10360.216
10370
1038-0.414
1039-0.186
1040
1040-0.0865
10410.0598



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: CNhs11137

Jaspar motifP-value
MA0002.20.00319
MA0003.10.286
MA0004.10.346
MA0006.10.929
MA0007.10.474
MA0009.10.543
MA0014.10.167
MA0017.10.801
MA0018.20.022
MA0019.10.424
MA0024.11.59965e-5
MA0025.10.00261
MA0027.10.701
MA0028.11.41051e-5
MA0029.10.14
MA0030.10.526
MA0031.10.421
MA0035.20.415
MA0038.10.794
MA0039.20.207
MA0040.10.971
MA0041.10.24
MA0042.10.737
MA0043.10.061
MA0046.19.59915e-17
MA0047.20.8
MA0048.10.613
MA0050.14.96881e-6
MA0051.15.00418e-5
MA0052.10.0131
MA0055.10.918
MA0057.10.701
MA0058.10.502
MA0059.10.00741
MA0060.10.0464
MA0061.14.27295e-5
MA0062.23.0166e-15
MA0065.20.501
MA0066.10.00692
MA0067.10.844
MA0068.10.491
MA0069.10.797
MA0070.10.444
MA0071.10.367
MA0072.11.42994e-5
MA0073.10.824
MA0074.10.895
MA0076.17.19693e-7
MA0077.10.146
MA0078.10.674
MA0079.20.0293
MA0080.25.79634e-13
MA0081.10.0261
MA0083.10.215
MA0084.10.351
MA0087.10.318
MA0088.10.258
MA0090.10.0411
MA0091.10.0317
MA0092.10.912
MA0093.10.398
MA0099.20.123
MA0100.10.0136
MA0101.19.0462e-5
MA0102.20.356
MA0103.13.91685e-4
MA0104.20.0826
MA0105.11.26197e-8
MA0106.10.727
MA0107.11.41736e-4
MA0108.20.0102
MA0111.10.326
MA0112.20.0107
MA0113.10.565
MA0114.10.372
MA0115.10.712
MA0116.10.00111
MA0117.10.619
MA0119.10.861
MA0122.10.921
MA0124.10.382
MA0125.10.51
MA0131.10.1
MA0135.10.196
MA0136.15.33999e-22
MA0137.20.0524
MA0138.28.57689e-6
MA0139.10.162
MA0140.10.745
MA0141.10.52
MA0142.10.607
MA0143.10.373
MA0144.10.405
MA0145.10.323
MA0146.10.531
MA0147.10.036
MA0148.10.757
MA0149.10.0584
MA0150.10.405
MA0152.10.813
MA0153.11.65081e-8
MA0154.10.11
MA0155.10.795
MA0156.12.41597e-24
MA0157.10.53
MA0159.10.132
MA0160.10.332
MA0162.10.422
MA0163.17.49012e-4
MA0164.10.729
MA0258.10.0316
MA0259.10.589



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: CNhs11137

Novel motifP-value
10.198
100.0106
1000.643
1010.997
1020.48
1030.191
1040.775
1050.957
1060.697
1070.975
1080.302
1090.287
110.105
1100.0454
1110.582
1120.207
1130.376
1140.685
1150.413
1160.672
1178.58091e-4
1180.247
1190.262
120.619
1200.192
1210.439
1220.659
1230.837
1240.699
1250.104
1260.429
1270.993
1280.548
1290.127
130.014
1300.332
1310.56
1320.699
1330.625
1340.325
1350.421
1360.309
1370.303
1380.723
1390.41
140.76
1400.87
1410.907
1420.644
1430.215
1440.194
1450.062
1460.716
1470.368
1480.256
1490.73
150.144
1500.365
1510.2
1520.0736
1530.224
1540.0472
1550.248
1560.0236
1570.45
1580.129
1590.0545
1600.848
1610.479
1620.458
1630.706
1640.144
1650.293
1660.546
1670.114
1680.474
1690.31
170.607
180.821
190.851
20.0848
200.267
210.42
220.882
230.899
240.169
250.235
260.0294
270.553
280.259
290.0397
30.123
300.153
310.449
320.123
330.419
340.951
350.0986
360.11
370.183
380.257
390.975
40.913
400.479
410.903
420.0243
430.397
440.811
450.751
460.11
470.323
480.202
490.171
50.29
500.975
510.947
520.225
530.987
540.268
550.301
560.725
570.19
580.244
590.844
60.233
600.917
610.0455
620.0824
630.511
640.627
650.499
660.607
670.685
680.348
690.513
70.106
700.38
710.0212
720.44
730.527
740.818
750.0259
760.0433
770.281
780.108
790.8
80.327
800.125
810.902
820.794
830.799
840.0438
850.82
860.265
870.125
880.294
890.472
90.262
900.0592
910.897
920.979
930.757
940.195
950.498
960.011
970.502
980.611
990.457



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: CNhs11137


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)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002370 (thymus)
0002390 (hematopoietic system)
0002405 (immune system)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0003104 (mesenchyme)
0003295 (pharyngeal gland)
0003351 (pharyngeal epithelium)
0003408 (gland of gut)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005058 (hemolymphoid system gland)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005428 (vagal neural crest)
0005562 (thymus primordium)
0005911 (endo-epithelium)
0006562 (pharynx)
0006598 (presumptive structure)
0007026 (primitive gut)
0007284 (presumptive neural plate)
0007690 (early pharyngeal endoderm)
0009113 (thymic region)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

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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