Personal tools

FF:1391-42E2

From FANTOM5_SSTAR

Revision as of 21:32, 16 October 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:testis, neonate N30
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuetestis
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

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008974
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{library_id}}} {{{accession_numbers}}}
Accession ID Mm9

Library idBAMCTSS
{{{library_id}}}
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

CNhs11130

01.145
10
100
1000
10000.456
10010.339
10020
1003-0.0132
10040
1005-0.0389
10060.27
10070.336
10080
10090.276
1010.0798
10100
10110.971
10120
1013-0.174
1014-0.0874
10150.494
1016-0.261
10170
10180
10190
1020
10200
10210
10220.312
10230
1024-0.14
10250
10261.077
10270
10280
1029-0.0661
1030.0521
10300.198
1031-0.517
1032-0.232
10330
10340
10350.702
1036-0.187
10370
1038-0.188
10390.18
1040
1040-0.269
10410.333



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



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: CNhs11130

Jaspar motifP-value
MA0002.20.176
MA0003.10.867
MA0004.10.431
MA0006.10.167
MA0007.10.985
MA0009.10.539
MA0014.10.473
MA0017.10.401
MA0018.28.65971e-12
MA0019.10.0575
MA0024.10.447
MA0025.10.73
MA0027.10.455
MA0028.10.00439
MA0029.10.704
MA0030.10.917
MA0031.10.387
MA0035.20.0216
MA0038.10.912
MA0039.20.118
MA0040.10.402
MA0041.10.206
MA0042.10.976
MA0043.19.71983e-4
MA0046.15.9641e-11
MA0047.20.00666
MA0048.10.0731
MA0050.11.88638e-4
MA0051.10.505
MA0052.10.824
MA0055.16.25948e-5
MA0057.10.546
MA0058.10.397
MA0059.10.0188
MA0060.17.00114e-7
MA0061.10.0124
MA0062.20.00182
MA0065.20.1
MA0066.10.715
MA0067.10.324
MA0068.10.867
MA0069.10.684
MA0070.10.864
MA0071.10.516
MA0072.10.693
MA0073.10.986
MA0074.10.939
MA0076.10.00156
MA0077.14.68677e-4
MA0078.18.22671e-10
MA0079.20.185
MA0080.22.22589e-7
MA0081.10.0567
MA0083.10.482
MA0084.10.621
MA0087.10.133
MA0088.10.0416
MA0090.10.687
MA0091.10.498
MA0092.10.0967
MA0093.10.519
MA0099.20.0721
MA0100.18.59338e-18
MA0101.10.181
MA0102.20.185
MA0103.10.874
MA0104.20.00167
MA0105.10.00694
MA0106.10.0331
MA0107.10.0128
MA0108.20.041
MA0111.10.365
MA0112.20.987
MA0113.10.72
MA0114.10.22
MA0115.10.27
MA0116.10.162
MA0117.10.851
MA0119.10.13
MA0122.10.868
MA0124.10.933
MA0125.10.149
MA0131.10.0471
MA0135.10.12
MA0136.18.90673e-4
MA0137.20.128
MA0138.20.0721
MA0139.10.194
MA0140.15.92681e-4
MA0141.10.387
MA0142.10.948
MA0143.13.43409e-4
MA0144.10.106
MA0145.10.00936
MA0146.10.00207
MA0147.10.00174
MA0148.10.00175
MA0149.10.387
MA0150.10.876
MA0152.10.212
MA0153.12.82563e-5
MA0154.10.0476
MA0155.10.191
MA0156.10.0534
MA0157.10.304
MA0159.10.234
MA0160.12.83736e-4
MA0162.10.928
MA0163.10.0172
MA0164.10.488
MA0258.10.305
MA0259.10.0236



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: CNhs11130

Novel motifP-value
10.585
100.107
1000.0524
1010.952
1020.182
1030.67
1040.739
1050.399
1064.07231e-4
1075.70932e-4
1080.27
1090.184
110.412
1100.285
1110.0206
1120.248
1130.405
1140.255
1150.951
1160.895
1170.00499
1180.142
1190.892
120.836
1200.968
1210.0404
1220.765
1230.33
1240.224
1250.927
1260.167
1270.878
1280.00326
1290.45
130.085
1300.983
1310.184
1320.699
1330.771
1340.575
1350.0318
1360.00101
1370.543
1380.614
1390.363
140.31
1400.949
1410.142
1420.713
1430.697
1440.163
1450.267
1460.796
1470.241
1480.0751
1490.0743
150.701
1500.2
1510.192
1520.431
1530.299
1540.725
1550.225
1560.0352
1570.783
1586.68628e-6
1590.22
1600.161
1610.166
1620.732
1630.366
1640.19
1650.469
1660.602
1670.67
1680.438
1690.515
170.646
180.884
190.762
26.26518e-4
200.00436
210.429
220.986
230.416
240.118
250.336
260.886
270.00867
280.9
290.0559
30.911
300.246
310.28
320.745
330.268
340.839
350.631
360.187
370.822
380.866
390.52
40.759
400.129
414.24996e-4
420.8
430.639
440.823
450.366
460.891
470.328
480.379
490.944
50.821
500.886
510.55
520.174
530.267
540.508
550.677
560.233
570.974
580.557
590.222
60.556
600.447
610.649
620.744
630.695
640.661
650.229
660.0452
670.639
680.319
690.192
70.637
700.374
710.983
720.262
730.523
740.894
750.366
760.0186
770.671
780.0079
790.604
80.0423
800.306
810.2
820.989
830.899
840.627
850.889
860.855
870.0214
880.78
890.578
90.738
900.591
910.211
920.666
930.237
940.824
950.0866
960.39
970.256
980.976
990.247



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: CNhs11130


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)
0000473 (testis)
0000991 (gonad)
0000479 (tissue)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011495 (mouse testis- neonate N30 sample)

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
UBERON:0009117 (indifferent gonad)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005564 (gonad primordium)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

{{{1}}} Accession numbers
MethodSample accession id
{{{2}}} 
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{4}}} {{{3}}}
Accession ID

Library idBAMCTSS
{{{4}}}
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:1391-42E2&oldid=3077238"