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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000079,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000473,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000991,UBERON:0001048,UBERON:0001062,UBERON:0001301,UBERON:0001343,UBERON:0002050,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003101,UBERON:0003133,UBERON:0003135,UBERON:0004111,UBERON:0004120,UBERON:0004176,UBERON:0004458,UBERON:0005156,UBERON:0005423,UBERON:0005564,UBERON:0005904,UBERON:0009117,UBERON:0009196
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002113,UBERON:0000473,UBERON:0002100,UBERON:0000483,UBERON:0000991,UBERON:0001301,UBERON:0001343,UBERON:0000926,UBERON:0000080,UBERON:0000479,UBERON:0000058,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000025,UBERON:0006555,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0000990,UBERON:0003914,UBERON:0005103,UBERON:0000083,UBERON:0002050,UBERON:0005423,UBERON:0002553,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0003135,UBERON:0000119,UBERON:0003103,UBERON:0009569,UBERON:0005291,UBERON:0003133,UBERON:0004175,UBERON:0005904,UBERON:0002323,UBERON:0000489,UBERON:0005177,UBERON:0003104,UBERON:0005172,UBERON:0000464,UBERON:0004458,UBERON:0009201,UBERON:0005256,UBERON:0001048,UBERON:0003918,UBERON:0006598,UBERON:0003886,UBERON:0004819,UBERON:0004910,UBERON:0004909,UBERON:0004176,UBERON:0005173,UBERON:0005154,UBERON:0005295,UBERON:0002532,UBERON:0006553,UBERON:0001008,UBERON:0003101,UBERON:0003074,UBERON:0004122,UBERON:0000079,UBERON:0002417,UBERON:0006947,UBERON:0000916,UBERON:0003887,UBERON:0002120,UBERON:0009142,UBERON:0003081,UBERON:0004054,UBERON:0003064,UBERON:0004875,UBERON:0009196,UBERON:0009117,UBERON:0004871,UBERON:0006603,UBERON:0004876,UBERON:0005564,UBERON:0005297,UBERON:0004872,UBERON:0005095,UBERON:0005721,UBERON:0005754,UBERON:0003060,UBERON:0007687,UBERON:0005294,UBERON:0010141,UBERON:0007297,UBERON:0005891
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=

Revision as of 18:13, 8 June 2012


Name:epididymis and seminiferous tubule, neonate N30
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueepididymis and seminiferous tubule
dev stage30 days neonate
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]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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

CNhs11199

00
10
100
1000
10000.337
10010.209
10020.0242
1003-0.00968
10040.0509
10050.229
10060.275
10070.0472
10080
10090.269
101-0.0484
10100
10110.024
10120.0509
10130.11
10140
1015-0.145
1016-0.107
10170
10180.0637
10190.0509
1020
10200
10210.138
10220.244
10230.0509
10240.12
10250
10260.516
10270.0509
10280.0509
10290.124
1031.021
10300.21
10310.0357
10320.0318
10330.0342
10340.124
10350.0187
10360.00302
10370.0509
1038-0.0447
10390.0332
1040
10400.0783
10410.708



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: CNhs11199

Jaspar motifP-value
MA0002.21.52627e-7
MA0003.10.00872
MA0004.10.218
MA0006.10.0905
MA0007.10.0272
MA0009.10.785
MA0014.10.705
MA0017.10.806
MA0018.21.45093e-5
MA0019.10.0579
MA0024.10.898
MA0025.10.297
MA0027.10.41
MA0028.10.0467
MA0029.10.492
MA0030.10.621
MA0031.10.591
MA0035.20.0352
MA0038.10.656
MA0039.20.0401
MA0040.10.0854
MA0041.10.354
MA0042.10.529
MA0043.11.73304e-5
MA0046.10.0021
MA0047.20.865
MA0048.10.459
MA0050.15.56981e-4
MA0051.10.0027
MA0052.14.41334e-12
MA0055.10.442
MA0057.10.321
MA0058.10.167
MA0059.10.179
MA0060.10.676
MA0061.10.215
MA0062.20.0301
MA0065.20.24
MA0066.10.662
MA0067.10.403
MA0068.10.00875
MA0069.10.671
MA0070.10.811
MA0071.10.982
MA0072.10.0629
MA0073.10.836
MA0074.10.935
MA0076.10.0205
MA0077.10.162
MA0078.10.0251
MA0079.20.972
MA0080.23.23998e-10
MA0081.10.141
MA0083.16.89132e-4
MA0084.10.863
MA0087.10.61
MA0088.10.883
MA0090.10.784
MA0091.10.241
MA0092.10.46
MA0093.10.197
MA0099.20.817
MA0100.10.814
MA0101.10.847
MA0102.20.137
MA0103.10.871
MA0104.20.0952
MA0105.10.11
MA0106.10.494
MA0107.10.735
MA0108.20.031
MA0111.10.763
MA0112.25.6601e-5
MA0113.10.00825
MA0114.10.187
MA0115.10.0233
MA0116.10.0469
MA0117.10.856
MA0119.10.0468
MA0122.10.411
MA0124.10.867
MA0125.10.054
MA0131.10.607
MA0135.10.922
MA0136.13.10583e-6
MA0137.20.0467
MA0138.20.94
MA0139.10.34
MA0140.12.30253e-11
MA0141.10.9
MA0142.10.696
MA0143.10.371
MA0144.10.903
MA0145.10.0615
MA0146.10.251
MA0147.10.106
MA0148.10.966
MA0149.10.566
MA0150.10.281
MA0152.10.98
MA0153.19.72368e-4
MA0154.10.00355
MA0155.10.304
MA0156.12.62969e-4
MA0157.10.494
MA0159.10.312
MA0160.10.859
MA0162.10.519
MA0163.10.00294
MA0164.10.287
MA0258.10.0068
MA0259.10.0533



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: CNhs11199

Novel motifP-value
10.537
100.589
1000.982
1010.84
1020.827
1030.334
1040.295
1050.425
1060.0078
1070.063
1080.414
1090.133
110.487
1100.303
1110.682
1120.108
1130.432
1140.799
1150.738
1160.363
1170.691
1180.75
1190.0686
120.353
1200.557
1210.421
1220.348
1230.515
1240.138
1250.238
1260.561
1270.76
1280.0229
1290.559
130.00665
1300.0508
1310.584
1320.974
1330.356
1340.236
1350.3
1360.63
1370.0274
1380.441
1390.879
140.332
1400.511
1410.825
1420.108
1430.155
1440.38
1450.197
1460.307
1470.88
1480.109
1490.00677
150.038
1500.409
1510.146
1520.0733
1530.69
1540.826
1550.965
1560.0213
1570.184
1580.922
1590.581
1600.288
1610.509
1620.618
1630.323
1640.266
1650.00137
1660.0881
1670.0874
1680.169
1699.79221e-4
170.236
180.543
190.0132
20.13
200.64
210.0739
220.139
230.159
240.0626
250.776
260.0152
270.439
280.671
290.427
30.242
300.521
310.536
320.00282
330.974
340.164
350.502
360.457
370.0763
380.409
390.0873
40.594
400.143
410.079
420.568
430.238
440.492
450.23
460.263
470.477
480.625
490.477
50.213
500.219
510.468
520.119
530.125
540.489
550.101
560.632
570.672
580.268
590.0118
60.0792
600.0466
610.795
620.151
630.106
640.882
650.292
660.823
670.554
680.987
690.00625
70.099
700.417
710.0977
720.649
730.12
740.315
750.455
760.423
770.398
780.0764
790.825
80.593
800.0664
810.335
820.188
830.28
840.639
850.0324
860.446
870.277
880.981
890.471
90.237
900.29
910.0326
920.326
930.545
940.169
950.259
960.418
970.429
980.523
990.477



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: CNhs11199


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
0000468 (multi-cellular organism)
0000922 (embryo)
0002113 (kidney)
0000473 (testis)
0002100 (trunk)
0000483 (epithelium)
0000991 (gonad)
0001301 (epididymis)
0001343 (seminiferous tubule of testis)
0000926 (mesoderm)
0000080 (mesonephros)
0000479 (tissue)
0000058 (duct)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000025 (tube)
0006555 (excretory tube)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0000990 (reproductive system)
0003914 (epithelial tube)
0005103 (mesonephric epithelium)
0000083 (mesonephric tubule)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0003135 (male reproductive organ)
0000119 (cell layer)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0003133 (reproductive organ)
0004175 (internal genitalia)
0005904 (duct of male reproductive system)
0002323 (body cavity)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0003104 (mesenchyme)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0009201 (nephric duct)
0005256 (trunk mesenchyme)
0001048 (primordium)
0003918 (kidney mesenchyme)
0006598 (presumptive structure)
0003886 (body cavity precursor)
0004819 (kidney epithelium)
0004910 (epithelium of male gonad)
0004909 (epithelium of gonad)
0004176 (external genitalia)
0005173 (abdominal segment element)
0005154 (epithelial cord)
0005295 (sex cord)
0002532 (epiblast (generic))
0006553 (renal duct)
0001008 (renal system)
0003101 (male organism)
0003074 (mesonephric duct)
0004122 (genitourinary system)
0000079 (male reproductive system)
0002417 (abdominal segment of trunk)
0006947 (male genital duct)
0000916 (abdomen)
0003887 (intraembryonic coelom)
0002120 (pronephros)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0004054 (internal male genitalia)
0003064 (intermediate mesoderm)
0004875 (nephrogenic cord)
0009196 (indifferent external genitalia)
0009117 (indifferent gonad)
0004871 (somatic layer of lateral plate mesoderm)
0006603 (presumptive mesoderm)
0004876 (urogenital ridge)
0005564 (gonad primordium)
0005297 (testis sex cord)
0004872 (splanchnic layer of lateral plate mesoderm)
0005095 (kidney rudiment)
0005721 (pronephric mesoderm)
0005754 (rostral part of nephrogenic cord)
0003060 (pronephric duct)
0007687 (kidney field)
0005294 (genital ridge)
0010141 (primitive sex cord of indifferent gonad)
0007297 (presumptive pronephric mesoderm)
0005891 (coelomic epithelium)

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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