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{{f5samples
{{f5samples
|id=FF:59-29C1
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000153,UBERON:0000161,UBERON:0000165,UBERON:0000166,UBERON:0000167,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000930,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001044,UBERON:0001048,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0001736,UBERON:0001829,UBERON:0002050,UBERON:0002330,UBERON:0002365,UBERON:0002530,UBERON:0002532,UBERON:0002553,UBERON:0003104,UBERON:0003293,UBERON:0003294,UBERON:0003408,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005423,UBERON:0006298,UBERON:0007023,UBERON:0007026,UBERON:0009142
|name=submandibular gland, adult
|sample_id=59
|rna_tube_id=29C1
|rna_box=29
|rna_position=C1
|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=submandibular 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=CNhs10469,LSID646,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
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|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:59-29C1
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011388
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011388
|name=submandibular gland, adult
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10469,LSID646,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=29
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=C1
|rna_rin=
|rna_sample_type=
|rna_tube_id=29C1
|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=59
|sample_note=
|sample_sex=male
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=submandibular gland
|top_motifs=bHLH_family:2.25156604815;FOXO1,3,4:2.21532691275;ATF6:2.21414494343;ALX1:2.18535278559;HAND1,2:2.1003865343;SNAI1..3:1.97962697295;TLX2:1.8855644112;ZEB1:1.69509924473;IRF7:1.55364747699;FOXQ1:1.5075396107;DMAP1_NCOR{1,2}_SMARC:1.49968179328;AR:1.30523994486;TP53:1.26324201346;POU2F1..3:1.22141484014;IRF1,2:0.964264841371;HIF1A:0.909510738727;ESRRA:0.896325300567;HMX1:0.861989172758;MYOD1:0.854494320147;FOXN1:0.850968670012;PAX1,9:0.75631483177;ETS1,2:0.754941205772;NFIX:0.749909384682;TEF:0.702747230169;TGIF1:0.680285652457;SP1:0.633281051965;NR1H4:0.628948518442;FOXP1:0.605216390374;XCPE1{core}:0.576078935426;HBP1_HMGB_SSRP1_UBTF:0.557498853569;SOX5:0.504005372734;LMO2:0.500386297072;ELF1,2,4:0.497527817777;ESR1:0.482468295859;DBP:0.440759305347;SPZ1:0.439813976853;FOX{D1,D2}:0.419671823365;SPIB:0.399161329776;MAFB:0.380176646938;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.378747550438;FOX{I1,J2}:0.361702452053;RUNX1..3:0.348339637292;PPARG:0.34044905856;SPI1:0.218763336517;CEBPA,B_DDIT3:0.211622437224;NFIL3:0.201724662168;MYBL2:0.165735099669;NANOG:0.134120191661;T:0.129031861783;GZF1:0.105521627411;NFATC1..3:0.0922433972573;ZBTB16:0.0872336410541;PAX4:0.0761386697432;STAT2,4,6:0.0720445265737;LHX3,4:0.068989712752;TFAP2{A,C}:0.0679886390655;TFAP4:0.0614994173314;NR6A1:0.0381291131544;REST:0.0193426482966;FOS_FOS{B,L1}_JUN{B,D}:0.0125044107009;SREBF1,2:0.0073891287437;NFKB1_REL_RELA:0.00416297896268;FOXM1:0.00174652617123;ADNP_IRX_SIX_ZHX:-0.00194251357932;GLI1..3:-0.00414123125327;FOXA2:-0.00414853896831;AIRE:-0.0219077120655;ATF2:-0.0269209597237;SRF:-0.106523087532;TEAD1:-0.115047791318;NHLH1,2:-0.130639336202;TBP:-0.138105630666;GTF2A1,2:-0.151805680559;PAX6:-0.158454998065;POU5F1:-0.160355232097;CREB1:-0.17388897593;HIC1:-0.19587369831;BPTF:-0.217265222779;NR5A1,2:-0.222517532249;CRX:-0.227281062795;STAT5{A,B}:-0.239532270756;GTF2I:-0.242609415534;ZNF148:-0.243242906762;ARID5B:-0.243564970516;PRDM1:-0.249422745871;MEF2{A,B,C,D}:-0.269136340598;NFE2L2:-0.271212961171;GCM1,2:-0.278875790051;NKX2-1,4:-0.294463444958;TFCP2:-0.300752789211;ELK1,4_GABP{A,B1}:-0.309187567698;TBX4,5:-0.310983425447;ATF5_CREB3:-0.327811079598;EP300:-0.345892547379;AHR_ARNT_ARNT2:-0.358507124249;TLX1..3_NFIC{dimer}:-0.363498158344;IKZF2:-0.366380804962;GATA4:-0.367610572311;ZNF143:-0.414108520597;MED-1{core}:-0.4144762341;OCT4_SOX2{dimer}:-0.416340327552;FOSL2:-0.417007901194;CDC5L:-0.423549406295;FOX{F1,F2,J1}:-0.423886807164;TFAP2B:-0.426523171731;HNF4A_NR2F1,2:-0.427606445533;RXRA_VDR{dimer}:-0.429239450784;FOXP3:-0.444394439562;SOX2:-0.463839514787;MYFfamily:-0.468302071007;HOXA9_MEIS1:-0.479203831943;MTF1:-0.492708825044;ZFP161:-0.497377137557;VSX1,2:-0.508527990494;BACH2:-0.512827273793;MTE{core}:-0.52290244608;NKX2-3_NKX2-5:-0.556143768129;PRRX1,2:-0.568600453746;JUN:-0.594638162582;HNF1A:-0.599644723217;GFI1:-0.602308129346;HMGA1,2:-0.603429365127;HOX{A4,D4}:-0.607907039729;POU6F1:-0.611928659423;SOX{8,9,10}:-0.614084677995;KLF4:-0.615251944119;SMAD1..7,9:-0.618253834085;NFE2L1:-0.636567105924;YY1:-0.644617074285;RFX2..5_RFXANK_RFXAP:-0.645625475973;TOPORS:-0.671595963815;RREB1:-0.671783575884;ZBTB6:-0.674046572804;POU3F1..4:-0.678539648002;NR3C1:-0.683671697317;RXR{A,B,G}:-0.69432912332;MAZ:-0.714629353659;BREu{core}:-0.723545290923;MZF1:-0.725576572297;ZNF384:-0.726713033873;FOXD3:-0.739221374773;MYB:-0.741583465574;HES1:-0.741886728065;NKX3-1:-0.750493958566;HLF:-0.759248497162;EBF1:-0.773562382382;PATZ1:-0.799839276117;RFX1:-0.803643255456;PDX1:-0.81032000792;PITX1..3:-0.821072999033;NANOG{mouse}:-0.851744965605;NRF1:-0.855666573823;GATA6:-0.857093344258;TAL1_TCF{3,4,12}:-0.861100118872;ATF4:-0.886907465347;ALX4:-0.893474819601;IKZF1:-0.937479198519;NKX6-1,2:-0.951312594015;RORA:-0.956076378782;NKX2-2,8:-0.962067026632;CDX1,2,4:-0.969509851794;PAX5:-0.975249006225;CUX2:-0.979321694116;PBX1:-1.01469801757;RBPJ:-1.05275088017;PAX2:-1.06885970668;SOX17:-1.07770760985;NFE2:-1.10136609571;POU1F1:-1.1028293371;EGR1..3:-1.11579810408;NKX3-2:-1.13180141913;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.13297427731;ONECUT1,2:-1.1489001136;NFY{A,B,C}:-1.16385414168;TFDP1:-1.19667500279;GFI1B:-1.19870026798;ZNF238:-1.21865785038;LEF1_TCF7_TCF7L1,2:-1.28909215103;E2F1..5:-1.29140751697;HOX{A5,B5}:-1.31562984483;EN1,2:-1.31995121552;UFEwm:-1.32575155526;EVI1:-1.33648886904;ZIC1..3:-1.48191610795;PAX8:-1.64159032757;FOXL1:-1.87139905138;STAT1,3:-1.92336696018;HSF1,2:-2.04425152795;ZNF423:-2.49011745673
}}
}}

Revision as of 15:35, 21 March 2012


Name:submandibular 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
tissuesubmandibular 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

CNhs10469

00
10
100
1000
10000
10010
1002-0.0663
10030.173
10040
10050.171
10060
1007-0.0396
10080
1009-0.0572
101-0.0707
10100
10110.12
10120
10130.556
1014-0.0874
1015-0.196
1016-0.255
10170
10180
10190
1020
10200
10210
10220.731
10230
1024-0.0899
10250
10260
1027-0.048
10280
10290.027
103-0.0787
10300
1031-0.417
10320.167
1033-0.0752
10340.728
10350
1036-0.233
10370.457
1038-0.0619
10390.194
1040
1040-0.0865
10410.21



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: CNhs10469

Jaspar motifP-value
MA0002.20.143
MA0003.10.135
MA0004.10.419
MA0006.10.351
MA0007.10.166
MA0009.10.0675
MA0014.10.195
MA0017.10.891
MA0018.20.0522
MA0019.19.21722e-4
MA0024.14.93387e-5
MA0025.10.489
MA0027.10.211
MA0028.10.57
MA0029.10.36
MA0030.10.598
MA0031.10.765
MA0035.20.0109
MA0038.10.533
MA0039.20.009
MA0040.10.682
MA0041.10.187
MA0042.10.661
MA0043.10.0123
MA0046.19.6203e-8
MA0047.20.326
MA0048.10.541
MA0050.10.00101
MA0051.10.172
MA0052.10.176
MA0055.10.899
MA0057.10.165
MA0058.10.544
MA0059.10.262
MA0060.11.48918e-5
MA0061.10.779
MA0062.20.406
MA0065.20.0582
MA0066.10.973
MA0067.10.19
MA0068.10.263
MA0069.10.854
MA0070.10.686
MA0071.10.574
MA0072.10.346
MA0073.10.559
MA0074.10.743
MA0076.10.434
MA0077.10.507
MA0078.10.438
MA0079.20.224
MA0080.22.55551e-7
MA0081.10.405
MA0083.10.18
MA0084.10.188
MA0087.10.665
MA0088.10.622
MA0090.10.768
MA0091.10.58
MA0092.10.312
MA0093.10.428
MA0099.20.673
MA0100.10.227
MA0101.10.878
MA0102.20.0556
MA0103.11.408e-6
MA0104.20.802
MA0105.10.238
MA0106.10.245
MA0107.10.926
MA0108.20.00492
MA0111.10.717
MA0112.22.33173e-5
MA0113.10.162
MA0114.10.809
MA0115.10.654
MA0116.10.665
MA0117.10.352
MA0119.10.457
MA0122.10.582
MA0124.10.259
MA0125.10.0961
MA0131.10.435
MA0135.10.953
MA0136.13.80647e-5
MA0137.20.717
MA0138.20.292
MA0139.10.694
MA0140.10.145
MA0141.13.27938e-4
MA0142.10.112
MA0143.10.077
MA0144.10.6
MA0145.14.39821e-4
MA0146.10.65
MA0147.10.791
MA0148.10.099
MA0149.10.743
MA0150.10.341
MA0152.10.433
MA0153.18.85292e-6
MA0154.10.0192
MA0155.10.371
MA0156.12.01714e-4
MA0157.10.394
MA0159.10.0196
MA0160.10.0239
MA0162.10.692
MA0163.10.692
MA0164.10.761
MA0258.10.0106
MA0259.10.837



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: CNhs10469

Novel motifP-value
10.11
100.117
1000.955
1010.176
1020.495
1030.0257
1040.496
1050.31
1060.017
1070.123
1080.946
1090.408
110.462
1100.393
1110.0234
1120.155
1130.308
1140.358
1150.53
1160.143
1170.461
1180.691
1190.0711
120.689
1200.693
1210.59
1220.167
1230.242
1240.342
1250.0956
1260.285
1270.087
1280.0597
1290.147
130.00151
1300.478
1310.525
1320.551
1330.112
1340.504
1350.879
1360.357
1370.864
1380.307
1390.334
140.544
1400.0729
1410.117
1420.409
1430.276
1440.528
1450.224
1460.579
1470.845
1480.918
1490.813
150.332
1500.132
1510.126
1520.0862
1530.588
1540.784
1550.292
1561.44495e-12
1570.382
1580.388
1590.143
1600.298
1610.999
1620.334
1630.611
1640.39
1650.633
1660.71
1670.726
1680.171
1690.0508
170.0806
180.9
190.16
20.673
200.749
210.815
220.377
230.232
240.0744
250.618
260.0057
270.522
280.631
290.839
30.497
300.357
310.723
320.724
330.636
340.913
350.479
360.572
370.0701
380.489
390.445
40.671
400.727
410.529
420.301
430.215
440.835
450.401
460.119
470.335
480.293
490.163
50.186
500.634
510.773
520.198
530.737
540.74
550.319
560.487
570.714
580.137
590.154
60.574
600.136
610.209
620.182
630.0747
640.972
650.233
660.636
670.735
680.432
690.665
70.144
700.00698
710.076
720.488
730.0829
740.945
750.244
760.414
770.371
780.226
790.691
80.826
800.69
810.987
820.205
830.683
840.25
850.00761
860.242
870.616
880.37
890.0492
90.547
900.527
910.413
920.726
930.0509
940.693
950.559
960.373
970.538
980.209
990.502



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: CNhs10469


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
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000153 (anterior region of body)
0000161 (orifice)
0000165 (mouth)
0000166 (oral opening)
0000167 (oral cavity)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000930 (stomodeum)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001044 (saliva-secreting gland)
0001048 (primordium)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0001736 (submandibular gland)
0001829 (major salivary gland)
0002050 (embryonic structure)
0002330 (exocrine system)
0002365 (exocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003293 (gland of oral region)
0003294 (gland of foregut)
0003408 (gland of gut)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0006298 (submandibular gland primordium)
0007023 (adult organism)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

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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