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{{f5samples
{{f5samples
|id=FF:57-7G5
|id=FF:57-7G5
|name=testis, adult, biol_rep1
|name=testis, adult
|sample_id=57
|sample_id=57
|rna_tube_id=57-7G5
|rna_tube_id=7G5
|rna_box=57-7G5
|rna_box=7
|rna_position=57-7G5
|rna_position=G5
|sample_cell_lot=
|sample_cell_lot=
|sample_cell_catalog=
|sample_cell_catalog=
Line 32: Line 32:
|rna_concentration=
|rna_concentration=
|sample_note=
|sample_note=
|profile_hcage=CNhs10504,LSID648,,COMPLETED
|profile_hcage=CNhs10504,LSID648,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:54, 27 February 2012


Name:testis, 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
tissuetestis
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

CNhs10504

01.43
10
100
1000
10000.343
10010.605
1002-0.0941
1003-0.102
10040
1005-0.0389
1006-0.143
10070.465
10080
10090.137
1010.122
10100
10111.457
10120
1013-0.217
1014-0.0874
10150.795
1016-0.351
10170
10180
10190
1020
10200
1021-0.0487
1022-0.06
10230
1024-0.113
10250
10261.392
1027-0.048
10280
1029-0.148
103-0.0848
10300
1031-0.953
1032-0.655
10330.0305
10340
10350.328
1036-0.493
10370
1038-0.398
10390.0338
1040
1040-0.866
10410.194



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: CNhs10504

Jaspar motifP-value
MA0002.20.463
MA0003.10.937
MA0004.10.425
MA0006.10.164
MA0007.10.83
MA0009.10.395
MA0014.10.556
MA0017.10.426
MA0018.21.5801e-12
MA0019.10.09
MA0024.10.328
MA0025.10.456
MA0027.10.459
MA0028.15.69831e-4
MA0029.10.662
MA0030.10.93
MA0031.10.518
MA0035.20.0311
MA0038.10.646
MA0039.20.259
MA0040.10.346
MA0041.10.193
MA0042.10.625
MA0043.17.66892e-5
MA0046.12.25439e-7
MA0047.20.0352
MA0048.10.0627
MA0050.11.91099e-4
MA0051.10.417
MA0052.10.00238
MA0055.18.76501e-5
MA0057.10.505
MA0058.10.34
MA0059.10.0162
MA0060.11.72528e-5
MA0061.10.0223
MA0062.21.82512e-5
MA0065.20.11
MA0066.10.879
MA0067.10.271
MA0068.10.634
MA0069.10.431
MA0070.10.968
MA0071.10.548
MA0072.10.742
MA0073.10.984
MA0074.10.798
MA0076.11.07128e-4
MA0077.15.57037e-5
MA0078.14.3804e-11
MA0079.20.0799
MA0080.23.97467e-5
MA0081.10.175
MA0083.10.0699
MA0084.10.367
MA0087.10.0437
MA0088.10.028
MA0090.10.438
MA0091.10.615
MA0092.10.0905
MA0093.10.509
MA0099.20.254
MA0100.11.11681e-16
MA0101.10.325
MA0102.20.213
MA0103.10.696
MA0104.20.00218
MA0105.10.0142
MA0106.10.0622
MA0107.10.029
MA0108.20.00152
MA0111.10.505
MA0112.20.455
MA0113.10.337
MA0114.10.447
MA0115.10.147
MA0116.10.168
MA0117.10.65
MA0119.10.0866
MA0122.10.714
MA0124.10.946
MA0125.10.217
MA0131.10.0673
MA0135.10.498
MA0136.10.174
MA0137.20.365
MA0138.20.0464
MA0139.10.2
MA0140.19.21469e-4
MA0141.10.593
MA0142.10.68
MA0143.11.17957e-4
MA0144.10.363
MA0145.10.0128
MA0146.10.00353
MA0147.10.00213
MA0148.10.0217
MA0149.10.255
MA0150.10.666
MA0152.10.116
MA0153.10.00136
MA0154.10.0436
MA0155.10.0971
MA0156.10.648
MA0157.10.437
MA0159.10.215
MA0160.10.00104
MA0162.10.974
MA0163.10.0289
MA0164.10.397
MA0258.10.773
MA0259.10.0212



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: CNhs10504

Novel motifP-value
10.581
100.137
1000.0907
1011
1020.194
1030.702
1040.735
1050.196
1067.53319e-4
1076.34182e-4
1080.466
1090.233
110.382
1100.38
1110.0188
1120.256
1130.388
1140.221
1150.947
1160.925
1170.00224
1180.177
1190.644
120.905
1200.834
1210.0265
1220.747
1230.357
1240.463
1250.839
1260.143
1270.996
1280.00307
1290.327
130.267
1300.589
1310.249
1320.536
1330.847
1340.806
1350.033
1360.00204
1370.603
1380.413
1390.459
140.219
1400.742
1410.169
1420.759
1430.993
1440.276
1450.384
1460.86
1470.254
1480.0582
1490.0637
150.672
1500.258
1510.18
1520.464
1530.323
1540.466
1550.106
1560.283
1570.911
1581.38217e-5
1590.166
1600.115
1610.127
1620.784
1630.515
1640.145
1650.349
1660.922
1670.286
1680.217
1690.954
170.603
180.892
190.394
29.7532e-4
200.00393
210.423
220.899
230.359
240.158
250.325
260.995
270.0182
280.949
290.0546
30.864
300.234
310.33
320.677
330.256
340.806
350.51
360.0863
370.91
380.794
390.373
40.813
400.108
413.08112e-4
420.875
430.569
440.933
450.341
460.933
470.312
480.335
490.896
50.742
500.707
510.56
520.146
530.226
540.428
550.97
560.243
570.968
580.571
590.237
60.596
600.403
610.659
620.66
630.569
640.613
650.289
660.0556
670.653
680.495
690.317
70.72
700.465
710.917
720.302
730.523
740.697
750.248
760.0148
770.525
780.0154
790.818
80.0459
800.252
810.201
820.935
830.669
840.678
850.809
860.704
870.0231
880.745
890.486
90.611
900.59
910.266
920.559
930.175
940.755
950.0877
960.443
970.241
980.92
990.232



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: CNhs10504


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000079 (male reproductive system)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000473 (testis)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000991 (gonad)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003101 (male organism)
0003133 (reproductive organ)
0003135 (male reproductive organ)
0004120 (mesoderm-derived structure)
0004176 (external genitalia)
0004458 (body cavity or lining)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005564 (gonad primordium)
0007023 (adult organism)
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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