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|library_id=CNhs10505
|library_id=CNhs10505
|library_id_phase_based=2:CNhs10505
|library_id_phase_based=2:CNhs10505
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/spinal%2520cord%252c%2520adult.CNhs10505.24-13C9.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/spinal%2520cord%252c%2520adult.CNhs10505.24-13C9.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spinal%2520cord%252c%2520adult.CNhs10505.24-13C9.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spinal%2520cord%252c%2520adult.CNhs10505.24-13C9.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spinal%2520cord%252c%2520adult.CNhs10505.24-13C9.mm9.nobarcode.rdna.fa.gz
|name=spinal cord, adult
|name=spinal cord, adult
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 18:01, 17 May 2017


Name:spinal cord, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10505
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuespinal cord
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005286
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10505 CAGE DRX009083 DRR009957
Accession ID Mm9

Library idBAMCTSS
CNhs10505 DRZ001382 DRZ002765
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs10505

00
10.726
100
1000
10000.117
10010.179
1002-0.00984
10030.171
10040
10050.035
10060.587
1007-0.0769
10080
1009-0.0676
101-0.0779
10100
10110.403
10120.19
10130.292
1014-0.0851
1015-0.116
1016-0.138
10170
10180
10190
1020
10200
1021-0.0487
10220.268
10230
10240.195
10250
10260.0644
10270.578
10280
10290.0932
103-0.0736
10300
1031-0.306
10320.438
1033-0.0665
10340
10350.137
1036-0.258
10370
1038-0.0134
10390.113
1040
1040-0.142
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



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: CNhs10505

Jaspar motifP-value
MA0002.20.00197
MA0003.10.369
MA0004.10.408
MA0006.10.283
MA0007.10.234
MA0009.10.708
MA0014.10.911
MA0017.12.46035e-6
MA0018.20.0136
MA0019.10.811
MA0024.10.0672
MA0025.10.00143
MA0027.10.137
MA0028.10.0721
MA0029.10.984
MA0030.10.598
MA0031.10.472
MA0035.20.0193
MA0038.10.242
MA0039.20.078
MA0040.10.56
MA0041.10.0875
MA0042.10.29
MA0043.10.0664
MA0046.15.04426e-11
MA0047.21.60614e-4
MA0048.10.0273
MA0050.16.03212e-4
MA0051.10.0044
MA0052.10.608
MA0055.10.0066
MA0057.10.27
MA0058.10.501
MA0059.10.104
MA0060.10.348
MA0061.10.024
MA0062.20.00145
MA0065.23.1389e-6
MA0066.10.0189
MA0067.10.271
MA0068.10.457
MA0069.10.136
MA0070.10.207
MA0071.10.0906
MA0072.10.602
MA0073.10.821
MA0074.10.0612
MA0076.10.176
MA0077.10.17
MA0078.10.681
MA0079.20.198
MA0080.23.51035e-9
MA0081.10.268
MA0083.10.0685
MA0084.10.591
MA0087.10.0672
MA0088.10.359
MA0090.10.0774
MA0091.10.192
MA0092.10.168
MA0093.10.509
MA0099.20.0233
MA0100.10.124
MA0101.10.0113
MA0102.20.544
MA0103.10.102
MA0104.20.579
MA0105.10.00119
MA0106.10.0535
MA0107.10.0345
MA0108.20.0129
MA0111.10.875
MA0112.20.00175
MA0113.10.377
MA0114.13.86651e-6
MA0115.15.44215e-5
MA0116.10.0422
MA0117.10.897
MA0119.10.132
MA0122.10.873
MA0124.10.358
MA0125.10.028
MA0131.10.736
MA0135.10.247
MA0136.11.7104e-11
MA0137.20.534
MA0138.28.39219e-5
MA0139.10.553
MA0140.14.80814e-5
MA0141.10.00981
MA0142.10.375
MA0143.10.912
MA0144.10.153
MA0145.10.276
MA0146.10.0411
MA0147.10.394
MA0148.17.90758e-4
MA0149.10.162
MA0150.10.372
MA0152.10.264
MA0153.17.49996e-12
MA0154.10.035
MA0155.10.574
MA0156.15.03258e-7
MA0157.10.293
MA0159.10.00486
MA0160.10.0259
MA0162.10.285
MA0163.13.1194e-4
MA0164.10.862
MA0258.10.0272
MA0259.10.602



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: CNhs10505

Novel motifP-value
10.304
100.0421
1000.271
1010.913
1020.9
1030.111
1040.983
1050.632
1060.0434
1070.127
1080.606
1090.0142
110.119
1100.0403
1110.196
1120.00771
1130.462
1140.492
1150.683
1160.266
1170.00292
1180.199
1190.186
120.749
1200.889
1210.76
1220.954
1237.07387e-5
1240.0229
1250.0785
1260.0232
1270.386
1280.0253
1290.467
133.27406e-7
1300.202
1310.426
1320.77
1330.543
1340.143
1350.0674
1360.138
1370.781
1380.988
1390.432
140.585
1400.113
1410.879
1420.424
1430.244
1440.798
1458.32693e-5
1460.502
1470.498
1480.998
1490.749
150.166
1500.0793
1510.916
1520.175
1530.864
1540.776
1550.48
1560.0343
1570.344
1580.33
1590.739
1600.188
1610.213
1620.742
1630.624
1640.0206
1650.515
1660.678
1670.989
1680.743
1690.00583
170.106
180.913
190.226
20.604
200.0134
210.183
220.238
230.815
240.0672
250.813
265.29694e-11
270.316
280.831
290.0225
30.12
300.832
310.716
320.63
330.145
340.904
351
360.122
370.0684
380.476
390.503
40.263
400.138
410.46
420.235
430.15
440.506
450.804
460.0254
470.641
480.41
490.136
50.237
500.28
510.721
520.434
530.3
540.874
550.989
560.565
570.48
580.337
590.156
60.867
600.0508
610.0831
620.229
630.195
640.632
650.387
660.803
670.967
680.355
690.577
70.0239
700.0746
710.00224
720.667
730.0682
740.811
750.0437
760.204
770.571
780.00334
790.1
80.0599
800.664
810.494
820.403
830.528
840.837
850.225
860.145
870.502
880.63
890.489
90.584
900.0621
910.0457
920.309
930.167
940.454
950.0803
960.513
970.895
980.687
990.54



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: CNhs10505


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)
0007023 (adult organism)
0002240 (spinal cord)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0000489 (cavitated compound organ)
0005174 (dorsal region element)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001137 (dorsum)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011305 (mouse spinal cord- adult 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:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006241 (future spinal cord)
UBERON:0003057 (chordal neural plate)
UBERON:0010316 (germ layer / neural crest)

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