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{{f5samples
{{f5samples
|id=FF:51-27F8
|ancestors_in_anatomy_facet=UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000079,UBERON:0000080,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000473,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000489,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000991,UBERON:0000998,UBERON:0001008,UBERON:0001048,UBERON:0001062,UBERON:0002050,UBERON:0002100,UBERON:0002113,UBERON:0002120,UBERON:0002323,UBERON:0002417,UBERON:0002530,UBERON:0002532,UBERON:0002553,UBERON:0003064,UBERON:0003081,UBERON:0003101,UBERON:0003103,UBERON:0003133,UBERON:0003135,UBERON:0003886,UBERON:0003887,UBERON:0003937,UBERON:0004054,UBERON:0004111,UBERON:0004120,UBERON:0004175,UBERON:0004176,UBERON:0004458,UBERON:0004875,UBERON:0004876,UBERON:0005095,UBERON:0005156,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005399,UBERON:0005423,UBERON:0005564,UBERON:0005721,UBERON:0005754,UBERON:0005904,UBERON:0006554,UBERON:0006868,UBERON:0006947,UBERON:0007023,UBERON:0007194,UBERON:0007687,UBERON:0009117,UBERON:0009196
|name=vesicular gland, adult
|sample_id=51
|rna_tube_id=27F8
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|rna_position=F8
|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=adult
|sample_tissue=vesicular gland
|sample_donor(cell lot)=
|sample_sex=male
|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=CNhs10491,LSID647,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000079,UBERON:0000080,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000473,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000489,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000991,UBERON:0000998,UBERON:0001008,UBERON:0001048,UBERON:0001062,UBERON:0002050,UBERON:0002100,UBERON:0002113,UBERON:0002120,UBERON:0002323,UBERON:0002417,UBERON:0002530,UBERON:0002532,UBERON:0002553,UBERON:0003064,UBERON:0003081,UBERON:0003101,UBERON:0003103,UBERON:0003133,UBERON:0003135,UBERON:0003886,UBERON:0003887,UBERON:0003937,UBERON:0004054,UBERON:0004111,UBERON:0004120,UBERON:0004175,UBERON:0004176,UBERON:0004458,UBERON:0004875,UBERON:0004876,UBERON:0005095,UBERON:0005156,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005399,UBERON:0005423,UBERON:0005564,UBERON:0005721,UBERON:0005754,UBERON:0005904,UBERON:0006554,UBERON:0006868,UBERON:0006947,UBERON:0007023,UBERON:0007194,UBERON:0007687,UBERON:0009117,UBERON:0009196
|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:51-27F8
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011380
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011380
|name=vesicular gland, adult
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=UBERON:0000998;;UBERON:0007194
|part_of=UBERON:0000998;;UBERON:0007194
|profile_cagescan=,,,
|profile_hcage=CNhs10491,LSID647,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=27
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=F8
|rna_rin=
|rna_sample_type=
|rna_tube_id=27F8
|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=adult
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=51
|sample_note=
|sample_sex=male
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=vesicular gland
|top_motifs=FOXO1,3,4:3.69639390786;FOXN1:2.48694982763;FOXQ1:2.10622546081;ATF6:2.08386109542;AR:1.55148887498;SNAI1..3:1.54362166048;ESR1:1.26259078013;HMX1:1.22133917703;FOXP1:1.15785678841;ZEB1:1.13937409002;FOXM1:1.09301006683;HIF1A:0.911614621759;AIRE:0.894164422042;GZF1:0.848100554068;HAND1,2:0.828159719187;MYOD1:0.782961084333;IRF1,2:0.756826233351;TP53:0.742547012446;TOPORS:0.73253051602;TBX4,5:0.7226978394;SRF:0.694377810167;SPZ1:0.68110900924;CDC5L:0.680211424282;ZBTB16:0.621789309444;NFATC1..3:0.581372580804;TLX2:0.560592963193;STAT2,4,6:0.522087250568;SOX5:0.497565545453;NKX3-2:0.494116388156;SREBF1,2:0.447009957994;CEBPA,B_DDIT3:0.411386752059;IRF7:0.356518456146;ESRRA:0.354999198618;FOX{I1,J2}:0.354662111621;T:0.34767966341;TFAP2{A,C}:0.336059446424;NKX2-1,4:0.33344757025;NFE2L1:0.315946101666;NR6A1:0.297642961523;TFAP4:0.282080538224;FOSL2:0.261664102554;ETS1,2:0.243183644115;HBP1_HMGB_SSRP1_UBTF:0.241148186276;ELF1,2,4:0.216448278524;ZNF148:0.188805152078;BACH2:0.174261442721;HES1:0.169169760635;ALX4:0.160607070721;bHLH_family:0.14657519898;LEF1_TCF7_TCF7L1,2:0.112566052612;STAT5{A,B}:0.109786033136;HIC1:0.10627871625;MAFB:0.104416543999;NKX6-1,2:0.103541572269;XCPE1{core}:0.0900072205441;NFE2L2:0.087901910964;TEAD1:0.087464804635;NANOG:0.067192714115;ATF5_CREB3:0.0519608260012;TLX1..3_NFIC{dimer}:0.0410951377498;GFI1B:0.0303944762291;SP1:0.0264778824175;FOXP3:0.0236578813503;DMAP1_NCOR{1,2}_SMARC:0.00742086840201;GTF2A1,2:0.00333267141044;FOX{D1,D2}:-0.00131615084229;ELK1,4_GABP{A,B1}:-0.0237975185899;GTF2I:-0.0432595995085;TGIF1:-0.0741505490314;AHR_ARNT_ARNT2:-0.0800074350824;VSX1,2:-0.0902124446147;FOXA2:-0.0969508281859;MED-1{core}:-0.0971379920587;FOS_FOS{B,L1}_JUN{B,D}:-0.123406419165;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.138191540128;HOXA9_MEIS1:-0.146625746691;SOX2:-0.149972406243;PITX1..3:-0.151897407972;ZIC1..3:-0.156487387661;NKX2-3_NKX2-5:-0.157894413187;TBP:-0.160049843592;RFX2..5_RFXANK_RFXAP:-0.166232070772;SMAD1..7,9:-0.166638344323;ADNP_IRX_SIX_ZHX:-0.169526986199;ZNF423:-0.177339155152;SPI1:-0.183173538335;CRX:-0.207241108075;REST:-0.21542061657;TFCP2:-0.234115501076;EVI1:-0.241377757952;MYBL2:-0.267469827261;NFKB1_REL_RELA:-0.267495349303;TFAP2B:-0.268064673661;CDX1,2,4:-0.271532152765;HMGA1,2:-0.295537989647;LHX3,4:-0.303365143583;BPTF:-0.317713234811;HNF1A:-0.31987830757;PRDM1:-0.335141657713;RUNX1..3:-0.338910430288;NKX2-2,8:-0.347446795094;SPIB:-0.369275795826;YY1:-0.369298320164;PAX1,9:-0.372723908033;MYB:-0.37763955197;ATF4:-0.37935565997;PAX5:-0.383270859601;NKX3-1:-0.392882171534;HNF4A_NR2F1,2:-0.404152391748;TEF:-0.411316204311;RORA:-0.4287175458;JUN:-0.435562070566;TAL1_TCF{3,4,12}:-0.442971917984;DBP:-0.459331304308;HLF:-0.469111246788;POU2F1..3:-0.470214484689;MTF1:-0.473128374609;ZFP161:-0.478574230599;NFIL3:-0.481606860019;MYFfamily:-0.489531183149;FOX{F1,F2,J1}:-0.492500949069;ZNF143:-0.494050996663;ATF2:-0.497793810804;MEF2{A,B,C,D}:-0.502978993283;ZBTB6:-0.509257812111;GLI1..3:-0.511447478335;RFX1:-0.519148547012;PAX2:-0.52578598068;PAX4:-0.528066045864;GCM1,2:-0.531268088167;OCT4_SOX2{dimer}:-0.532180075827;ONECUT1,2:-0.534563073857;NHLH1,2:-0.538577393598;MZF1:-0.543097283798;GATA6:-0.544132389415;PRRX1,2:-0.548474679111;KLF4:-0.553737834017;MAZ:-0.561827292311;CREB1:-0.583506806702;UFEwm:-0.58380295459;NFE2:-0.587065847265;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.59341301156;IKZF1:-0.595087322116;EGR1..3:-0.612634370268;LMO2:-0.61409734866;RXRA_VDR{dimer}:-0.618883712861;PATZ1:-0.64155308641;GATA4:-0.655524338119;BREu{core}:-0.658439979796;NR1H4:-0.664667278102;PDX1:-0.665856499182;POU5F1:-0.671089948242;STAT1,3:-0.676509899327;POU6F1:-0.687136104398;ARID5B:-0.688363020719;ZNF238:-0.704914520046;EBF1:-0.7235285961;NFY{A,B,C}:-0.751214003249;NRF1:-0.780375640661;NR3C1:-0.792318230177;RREB1:-0.82547748868;RBPJ:-0.908089113985;HSF1,2:-0.937472309234;TFDP1:-0.99659741183;FOXD3:-1.00761804708;CUX2:-1.03362071019;POU1F1:-1.06750080536;RXR{A,B,G}:-1.07237766551;IKZF2:-1.07555591141;EP300:-1.10405031082;MTE{core}:-1.11081241882;FOXL1:-1.11406701716;ZNF384:-1.1151829593;SOX17:-1.15928848052;PAX8:-1.24742624702;PBX1:-1.27389004814;POU3F1..4:-1.28973193237;PPARG:-1.29741469205;NR5A1,2:-1.31105258416;GFI1:-1.312374456;NFIX:-1.37016033156;PAX6:-1.37669347153;SOX{8,9,10}:-1.39381169061;E2F1..5:-1.46640635477;ALX1:-1.53258626666;EN1,2:-1.59374629271;HOX{A5,B5}:-1.62588984938;HOX{A4,D4}:-1.80046511205;NANOG{mouse}:-2.48029143287
}}
}}

Revision as of 15:35, 21 March 2012


Name:vesicular gland, adult
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuevesicular gland
dev stageadult
sexmale
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

CNhs10491

00
10
100
1000
10000.239
10010.0998
1002-0.0941
10030.077
10040
1005-0.0389
1006-0.143
10070.0202
10080
1009-0.0723
101-0.0628
10100
10110
10120
10130.732
1014-0.0874
1015-0.235
1016-0.289
10170
10180.0102
10190
1020
10200
10210
10220.423
10230
1024-0.0899
10250
10260
10270
10280
10295.646328e-4
103-0.0736
10300
1031-0.243
10320.211
10330
10340.187
10350
1036-0.22
10371.257
1038-0.0104
1039-0.0328
1040
10400.0547
10410.7



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: CNhs10491

Jaspar motifP-value
MA0002.20.187
MA0003.10.37
MA0004.10.296
MA0006.10.329
MA0007.13.78033e-4
MA0009.10.852
MA0014.10.315
MA0017.10.647
MA0018.20.00301
MA0019.10.691
MA0024.18.73806e-9
MA0025.10.105
MA0027.10.88
MA0028.10.503
MA0029.10.359
MA0030.10.983
MA0031.10.119
MA0035.20.33
MA0038.10.0271
MA0039.20.431
MA0040.10.957
MA0041.10.237
MA0042.10.473
MA0043.10.124
MA0046.10.0332
MA0047.20.00971
MA0048.10.891
MA0050.16.57953e-4
MA0051.10.00474
MA0052.10.0188
MA0055.10.943
MA0057.10.62
MA0058.10.265
MA0059.10.619
MA0060.17.67211e-7
MA0061.10.548
MA0062.20.906
MA0065.20.733
MA0066.10.794
MA0067.10.227
MA0068.10.617
MA0069.10.559
MA0070.10.75
MA0071.10.145
MA0072.10.581
MA0073.10.988
MA0074.10.254
MA0076.10.136
MA0077.10.0372
MA0078.10.172
MA0079.20.687
MA0080.20.0425
MA0081.10.282
MA0083.10.474
MA0084.10.806
MA0087.10.815
MA0088.10.827
MA0090.10.977
MA0091.10.139
MA0092.10.333
MA0093.10.367
MA0099.20.245
MA0100.10.577
MA0101.10.582
MA0102.20.054
MA0103.18.95768e-5
MA0104.20.894
MA0105.10.457
MA0106.10.316
MA0107.10.67
MA0108.20.0203
MA0111.10.451
MA0112.23.23947e-4
MA0113.10.535
MA0114.10.29
MA0115.10.48
MA0116.10.977
MA0117.10.174
MA0119.10.3
MA0122.10.749
MA0124.10.103
MA0125.10.257
MA0131.10.371
MA0135.10.475
MA0136.10.0783
MA0137.20.0157
MA0138.20.701
MA0139.10.0485
MA0140.10.787
MA0141.10.802
MA0142.10.913
MA0143.10.165
MA0144.11.36505e-4
MA0145.10.0355
MA0146.10.278
MA0147.10.819
MA0148.10.0429
MA0149.10.581
MA0150.10.14
MA0152.10.597
MA0153.10.0146
MA0154.10.48
MA0155.10.426
MA0156.10.314
MA0157.10.0812
MA0159.10.286
MA0160.10.372
MA0162.10.679
MA0163.10.154
MA0164.10.261
MA0258.10.0663
MA0259.10.927



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: CNhs10491

Novel motifP-value
10.0695
100.191
1000.735
1010.458
1020.413
1030.0605
1040.924
1050.217
1060.0116
1070.466
1080.284
1090.415
110.0897
1100.329
1110.00664
1120.0498
1130.402
1140.525
1150.134
1160.368
1170.501
1180.717
1190.0224
120.269
1200.785
1210.533
1220.792
1230.926
1240.918
1250.322
1260.73
1270.792
1280.0315
1290.227
130.0187
1300.0313
1310.691
1320.351
1330.545
1340.763
1350.517
1360.66
1370.649
1380.233
1390.415
140.988
1400.0505
1410.712
1420.634
1430.527
1440.0268
1450.0266
1460.264
1473.39985e-8
1480.34
1490.752
150.391
1500.103
1510.441
1520.0528
1530.433
1540.149
1550.55
1560.101
1570.883
1580.731
1590.921
1600.703
1610.171
1620.411
1630.409
1640.0294
1650.16
1660.93
1670.229
1680.419
1690.0541
170.0102
180.25
190.0108
20.147
200.886
210.466
220.155
230.0751
240.0869
250.429
260.0089
270.294
280.721
290.167
30.145
300.944
310.268
320.465
330.367
340.113
350.275
360.42
370.0797
380.253
390.0182
40.857
400.452
410.742
420.323
430.274
440.797
450.868
460.0654
470.269
480.199
490.192
50.227
500.356
510.651
520.196
530.554
540.662
550.374
560.84
570.327
580.224
590.545
60.18
600.0304
610.635
620.313
630.0805
640.36
650.0666
660.267
670.726
680.652
694.4459e-13
70.352
700.00568
710.0716
720.489
730.0158
740.0054
750.227
760.943
770.297
780.194
790.505
80.384
800.429
810.827
820.0322
830.0347
840.128
850.0435
860.146
870.889
880.622
890.304
90.57
900.399
910.188
920.214
930.143
940.961
950.911
960.331
970.0459
980.358
990.997



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: CNhs10491


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
0000058 (duct)
0000061 (anatomical structure)
0000062 (organ)
0000079 (male reproductive system)
0000080 (mesonephros)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000473 (testis)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000489 (cavitated compound organ)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000991 (gonad)
0000998 (seminal vesicle)
0001008 (renal system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002100 (trunk)
0002113 (kidney)
0002120 (pronephros)
0002323 (body cavity)
0002417 (abdominal segment of trunk)
0002530 (gland)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003064 (intermediate mesoderm)
0003081 (lateral plate mesoderm)
0003101 (male organism)
0003103 (compound organ)
0003133 (reproductive organ)
0003135 (male reproductive organ)
0003886 (body cavity precursor)
0003887 (intraembryonic coelom)
0003937 (sex gland)
0004054 (internal male genitalia)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004175 (internal genitalia)
0004176 (external genitalia)
0004458 (body cavity or lining)
0004875 (nephrogenic cord)
0004876 (urogenital ridge)
0005095 (kidney rudiment)
0005156 (reproductive structure)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005399 (male reproductive gland)
0005423 (developing anatomical structure)
0005564 (gonad primordium)
0005721 (pronephric mesoderm)
0005754 (rostral part of nephrogenic cord)
0005904 (duct of male reproductive system)
0006554 (urinary system structure)
0006868 (seminal fluid secreting gland)
0006947 (male genital duct)
0007023 (adult organism)
0007194 (vesicular gland)
0007687 (kidney field)
0009117 (indifferent gonad)
0009196 (indifferent external genitalia)

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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