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{{f5samples
{{f5samples
|id=FF:21-1G8
|ancestors_in_anatomy_facet=UBERON:0000007,UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000949,UBERON:0000955,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001890,UBERON:0001894,UBERON:0002050,UBERON:0002346,UBERON:0002368,UBERON:0002530,UBERON:0002532,UBERON:0002616,UBERON:0002780,UBERON:0003056,UBERON:0003075,UBERON:0003080,UBERON:0003296,UBERON:0004121,UBERON:0005068,UBERON:0005291,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007023,UBERON:0007135,UBERON:0007284
|name=pituitary gland, adult
|sample_id=21
|rna_tube_id=1G8
|rna_box=1
|rna_position=G8
|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=pituitary 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=CNhs10493,LSID647,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000007,UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000949,UBERON:0000955,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001890,UBERON:0001894,UBERON:0002050,UBERON:0002346,UBERON:0002368,UBERON:0002530,UBERON:0002532,UBERON:0002616,UBERON:0002780,UBERON:0003056,UBERON:0003075,UBERON:0003080,UBERON:0003296,UBERON:0004121,UBERON:0005068,UBERON:0005291,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007023,UBERON:0007135,UBERON:0007284
|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:21-1G8
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011303
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011303
|name=pituitary gland, adult
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10493,LSID647,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=1
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=G8
|rna_rin=
|rna_sample_type=
|rna_tube_id=1G8
|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=21
|sample_note=
|sample_sex=male
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=pituitary gland
|top_motifs=FOXN1:3.27152441004;RFX2..5_RFXANK_RFXAP:2.73101407071;CREB1:2.57683592521;RXRA_VDR{dimer}:2.22064700772;LHX3,4:2.0473438993;ATF6:1.98755022637;TBX4,5:1.96118455205;ARID5B:1.94977552392;AR:1.94549526223;FOXP1:1.93019550534;GCM1,2:1.84205526171;LMO2:1.84048439312;RFX1:1.8275991372;POU6F1:1.65784065155;ALX1:1.59299550891;CRX:1.52665735911;MAFB:1.51508525354;HAND1,2:1.50694746323;NHLH1,2:1.480709077;POU1F1:1.40676551593;PRRX1,2:1.29473417011;NRF1:1.28704523885;EGR1..3:1.28606726657;HBP1_HMGB_SSRP1_UBTF:1.20465777025;REST:1.1648945714;OCT4_SOX2{dimer}:1.09143169426;MYOD1:1.08405981781;ZEB1:1.07111145131;AHR_ARNT_ARNT2:1.05622272114;ATF5_CREB3:1.03349126508;BPTF:1.01911873406;ELK1,4_GABP{A,B1}:1.00362076435;MYFfamily:0.996561620258;SREBF1,2:0.991456052085;STAT2,4,6:0.963786786741;FOXD3:0.955439035222;IRF1,2:0.94697580409;ADNP_IRX_SIX_ZHX:0.946318340955;ZNF143:0.92582400547;SNAI1..3:0.912795510494;ZFP161:0.912775256735;NFIL3:0.894462962139;RBPJ:0.887305599731;FOXQ1:0.885519474483;FOXA2:0.883166448285;SPZ1:0.878704420058;ATF2:0.857328319683;EP300:0.811114559051;YY1:0.791241993567;JUN:0.773697776576;NANOG:0.76798241893;CUX2:0.759667938851;TGIF1:0.753548908549;HIC1:0.738724557679;STAT1,3:0.724909983651;PAX6:0.696014833757;TAL1_TCF{3,4,12}:0.669996411167;GZF1:0.645649057354;MTF1:0.615778027426;FOX{D1,D2}:0.615103367158;TEF:0.610077965819;ONECUT1,2:0.593245215236;SP1:0.573871385068;PBX1:0.571685113082;TFAP2B:0.546599484002;MED-1{core}:0.510931042484;FOXP3:0.495950993473;RORA:0.490021856365;ZBTB6:0.464854673597;PAX2:0.464185976535;ESRRA:0.435590716469;PAX5:0.429224939534;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.428993993674;BREu{core}:0.382681239304;NFY{A,B,C}:0.359217722308;GTF2I:0.336626002409;ZBTB16:0.33297537319;VSX1,2:0.320167331253;NR5A1,2:0.316872416823;BACH2:0.311780966734;XCPE1{core}:0.310194720229;AIRE:0.301010756643;NFE2:0.274474845114;SMAD1..7,9:0.267252616383;PRDM1:0.253760777787;GTF2A1,2:0.248221031493;PAX8:0.22264460614;GFI1B:0.2023943087;CDX1,2,4:0.188028144946;FOX{I1,J2}:0.172689524684;MZF1:0.16839414;NFIX:0.165061559601;TLX2:0.159874776035;FOS_FOS{B,L1}_JUN{B,D}:0.147093558195;NKX2-3_NKX2-5:0.14376535496;NKX3-1:0.136663121462;SOX{8,9,10}:0.123610532049;MTE{core}:0.10668386769;ZIC1..3:0.079369255714;PITX1..3:0.0716804668004;EBF1:0.0634089615965;RREB1:0.0516923880173;DBP:0.0501247965225;IRF7:0.0432391674314;TOPORS:0.0397458885301;ESR1:0.038211355385;MYBL2:0.0369250646748;HOXA9_MEIS1:0.0361342661752;PATZ1:0.0184558271079;ZNF384:0.0151382836283;MAZ:-0.00670236746391;ATF4:-0.0149073436747;KLF4:-0.0263488007211;HMGA1,2:-0.0302111614019;PAX1,9:-0.0395064711039;NKX6-1,2:-0.0423089195493;FOX{F1,F2,J1}:-0.0484510403875;CEBPA,B_DDIT3:-0.0657016146888;HMX1:-0.0836174842475;TFAP4:-0.104100473569;NFE2L2:-0.104540719411;LEF1_TCF7_TCF7L1,2:-0.109488289168;STAT5{A,B}:-0.124330131959;TP53:-0.136116410273;SOX5:-0.17853210743;HSF1,2:-0.185909515854;ELF1,2,4:-0.191800607626;DMAP1_NCOR{1,2}_SMARC:-0.193870612504;EN1,2:-0.204016904648;TFCP2:-0.263659900751;GLI1..3:-0.277926906734;NKX3-2:-0.312799813781;FOXM1:-0.319815154082;FOXO1,3,4:-0.31989965948;NKX2-1,4:-0.333206193438;SOX2:-0.34545578746;FOSL2:-0.378181133989;HIF1A:-0.380996210857;ETS1,2:-0.422480352584;NFKB1_REL_RELA:-0.444324368196;bHLH_family:-0.444432698022;MEF2{A,B,C,D}:-0.45490858224;SPIB:-0.491108973515;HLF:-0.498339424332;HOX{A5,B5}:-0.501390184445;MYB:-0.50690865264;TFAP2{A,C}:-0.513020913677;IKZF2:-0.532777942379;POU2F1..3:-0.576145750087;GFI1:-0.588934497881;PDX1:-0.6110946283;NFE2L1:-0.630853652551;CDC5L:-0.644872248781;PAX4:-0.647727453661;ZNF238:-0.681445193039;TBP:-0.681995172237;SPI1:-0.696995336525;TLX1..3_NFIC{dimer}:-0.707543511196;NR3C1:-0.710624605361;GATA6:-0.718498778449;TFDP1:-0.720565466307;ZNF423:-0.738786887919;TEAD1:-0.743118816484;HNF1A:-0.750540124833;NFATC1..3:-0.776915252094;HES1:-0.78781645098;HNF4A_NR2F1,2:-0.790890163812;T:-0.807424295555;NANOG{mouse}:-0.820150029095;RUNX1..3:-0.837368214302;HOX{A4,D4}:-0.902790009276;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.925309677809;EVI1:-0.965049872905;PPARG:-0.972887862294;ALX4:-1.04097481834;POU5F1:-1.04128840392;GATA4:-1.05129048393;ZNF148:-1.08351719475;NKX2-2,8:-1.08421253472;SRF:-1.09209665256;IKZF1:-1.15330204178;SOX17:-1.17900770785;UFEwm:-1.20249560322;POU3F1..4:-1.20663530381;NR1H4:-1.2212957909;RXR{A,B,G}:-1.24698867658;E2F1..5:-1.39481077569;FOXL1:-1.89607457297;NR6A1:-1.99682611864
}}
}}

Revision as of 15:33, 21 March 2012


Name:pituitary 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
tissuepituitary 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

CNhs10493

00
10.226
100
1000
10000
10010.159
1002-0.116
10030.147
10040.306
10050
10060.5
1007-0.079
10080
1009-0.0342
101-0.0544
10100
10110.0946
10120
10130.348
10140.337
1015-0.158
1016-0.108
10170
10180
10190
1020
10200
10210.0444
10220.361
10230
10240
1025-0.0611
10260
10270
10280
10290.0779
103-0.0802
10300
1031-0.199
10320.198
10330.251
10340
10350
1036-0.0297
10370
1038-0.0548
10390.261
1040
1040-0.167
10410



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: CNhs10493

Jaspar motifP-value
MA0002.28.47939e-4
MA0003.10.0355
MA0004.10.621
MA0006.10.251
MA0007.10.301
MA0009.10.8
MA0014.10.82
MA0017.11.29577e-7
MA0018.24.22184e-7
MA0019.10.459
MA0024.10.0168
MA0025.10.0654
MA0027.10.477
MA0028.10.173
MA0029.10.527
MA0030.10.99
MA0031.10.212
MA0035.20.00208
MA0038.10.254
MA0039.20.634
MA0040.10.571
MA0041.10.507
MA0042.10.683
MA0043.10.00182
MA0046.17.05802e-16
MA0047.20.00216
MA0048.10.0156
MA0050.16.74244e-4
MA0051.14.82479e-4
MA0052.10.0026
MA0055.10.255
MA0057.10.359
MA0058.10.939
MA0059.10.269
MA0060.10.0692
MA0061.10.0064
MA0062.20.114
MA0065.25.65108e-7
MA0066.18.73688e-4
MA0067.10.281
MA0068.10.687
MA0069.10.149
MA0070.10.346
MA0071.10.316
MA0072.10.776
MA0073.10.901
MA0074.10.126
MA0076.10.0226
MA0077.10.186
MA0078.10.046
MA0079.20.421
MA0080.21.04429e-6
MA0081.10.356
MA0083.19.3265e-4
MA0084.10.925
MA0087.10.959
MA0088.10.811
MA0090.10.138
MA0091.10.42
MA0092.10.294
MA0093.10.881
MA0099.20.134
MA0100.10.742
MA0101.10.0941
MA0102.20.804
MA0103.10.133
MA0104.20.548
MA0105.12.80736e-5
MA0106.10.255
MA0107.10.0421
MA0108.26.84254e-6
MA0111.10.619
MA0112.21.47088e-4
MA0113.10.824
MA0114.19.69309e-7
MA0115.11.56764e-4
MA0116.10.0143
MA0117.10.0539
MA0119.10.0131
MA0122.10.921
MA0124.10.71
MA0125.10.236
MA0131.10.938
MA0135.10.949
MA0136.15.74049e-4
MA0137.20.214
MA0138.20.0148
MA0139.10.404
MA0140.10.00144
MA0141.10.0118
MA0142.10.197
MA0143.10.335
MA0144.10.842
MA0145.10.425
MA0146.10.454
MA0147.10.395
MA0148.10.029
MA0149.10.577
MA0150.10.385
MA0152.10.909
MA0153.11.71571e-12
MA0154.10.0103
MA0155.10.0861
MA0156.10.455
MA0157.10.503
MA0159.10.0225
MA0160.10.107
MA0162.10.015
MA0163.18.5232e-4
MA0164.10.563
MA0258.10.00573
MA0259.10.743



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: CNhs10493

Novel motifP-value
10.147
100.0578
1000.743
1010.912
1020.593
1030.39
1040.681
1050.162
1066.11841e-4
1070.00602
1080.454
1090.109
110.167
1100.0563
1110.99
1120.219
1130.699
1140.902
1150.258
1160.0274
1170.0513
1180.704
1190.251
120.739
1200.76
1210.775
1220.0619
1230.458
1240.571
1250.29
1260.237
1270.0347
1280.0178
1290.776
130.00326
1300.555
1310.518
1320.717
1330.528
1340.755
1350.837
1360.842
1370.608
1380.142
1390.442
140.692
1400.752
1410.951
1420.298
1430.04
1440.826
1450.00966
1460.616
1470.765
1480.293
1490.473
150.255
1500.0662
1510.856
1520.219
1530.564
1540.936
1550.262
1560.00791
1570.386
1580.677
1590.0629
1600.0797
1610.58
1620.674
1630.831
1640.252
1650.0563
1660.258
1670.945
1680.719
1690.00384
170.247
180.5
190.096
20.59
200.59
210.331
220.186
230.382
240.215
250.82
269.54292e-4
270.727
280.829
290.19
30.276
300.778
310.923
320.0242
330.518
340.223
350.702
360.769
370.121
380.517
390.323
40.101
400.406
410.127
420.435
430.0863
440.238
450.403
460.0584
470.859
480.28
490.206
50.0498
500.298
510.583
520.0646
530.88
540.417
550.136
560.686
570.3
580.55
590.0171
60.487
600.0155
610.235
620.208
630.154
640.705
650.177
660.531
670.789
680.542
690.256
70.0963
700.788
710.00307
720.669
730.195
740.227
750.152
760.995
770.0803
782.62307e-4
790.853
80.0601
800.454
810.527
820.334
830.129
840.347
850.179
860.315
870.813
880.634
890.801
90.446
900.44
910.0659
920.176
930.203
940.59
950.249
960.546
970.328
980.937
990.0918



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: CNhs10493


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
0000007 (pituitary gland)
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000949 (endocrine system)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001890 (forebrain)
0001894 (diencephalon)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003296 (gland of diencephalon)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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