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FF:19-21D8

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Name:corpus striatum, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10487
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuecorpus striatum
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  SAMD00004779
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10487 CAGE DRX008945 DRR009819
Accession ID Mm9

Library idBAMCTSS
CNhs10487 DRZ001244 DRZ002627
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

CNhs10487

00
10.749
100
1000
10000
10010.0819
1002-0.0941
10030.103
10040
10050.125
10060.631
10070.0436
10080
1009-0.0572
101-0.057
10100
10110.948
10120.452
10130.179
1014-0.0851
1015-0.0207
10160.00992
10170
10180
10190
1020
10200
1021-0.0487
10220.058
10230
10240.0737
10250
10260
10270.193
10280
10290.0488
103-0.0861
10300
1031-0.338
10320.203
10330
10340
10350
1036-0.223
10370
1038-0.059
10390.103
1040
1040-0.216
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: CNhs10487

Jaspar motifP-value
MA0002.20.0105
MA0003.10.342
MA0004.10.59
MA0006.10.126
MA0007.10.45
MA0009.10.885
MA0014.10.641
MA0017.17.89366e-7
MA0018.20.00334
MA0019.10.475
MA0024.10.0232
MA0025.13.19862e-4
MA0027.10.0613
MA0028.10.044
MA0029.10.992
MA0030.10.773
MA0031.10.21
MA0035.20.0268
MA0038.10.398
MA0039.20.0264
MA0040.10.308
MA0041.10.0252
MA0042.10.225
MA0043.10.0214
MA0046.11.55268e-9
MA0047.25.29828e-4
MA0048.10.0238
MA0050.10.00191
MA0051.10.0399
MA0052.10.998
MA0055.10.00297
MA0057.10.479
MA0058.10.476
MA0059.10.148
MA0060.10.534
MA0061.10.0486
MA0062.26.40671e-4
MA0065.25.59256e-6
MA0066.10.0376
MA0067.10.522
MA0068.10.302
MA0069.10.0721
MA0070.10.363
MA0071.10.0349
MA0072.10.363
MA0073.10.905
MA0074.10.112
MA0076.10.103
MA0077.10.648
MA0078.10.935
MA0079.20.342
MA0080.26.93201e-10
MA0081.10.343
MA0083.10.0269
MA0084.10.852
MA0087.10.257
MA0088.10.337
MA0090.10.197
MA0091.10.148
MA0092.10.193
MA0093.10.643
MA0099.20.00857
MA0100.10.259
MA0101.10.0202
MA0102.20.426
MA0103.10.234
MA0104.20.909
MA0105.10.0173
MA0106.10.0477
MA0107.10.0598
MA0108.29.73762e-4
MA0111.10.762
MA0112.20.00132
MA0113.10.563
MA0114.17.01942e-6
MA0115.11.40044e-4
MA0116.10.0776
MA0117.10.928
MA0119.10.156
MA0122.10.545
MA0124.10.364
MA0125.10.0328
MA0131.10.516
MA0135.10.27
MA0136.15.5405e-13
MA0137.20.132
MA0138.24.66998e-5
MA0139.10.604
MA0140.11.88748e-4
MA0141.10.00151
MA0142.10.0973
MA0143.10.933
MA0144.10.0966
MA0145.10.191
MA0146.10.0176
MA0147.10.765
MA0148.10.00155
MA0149.10.132
MA0150.10.182
MA0152.10.256
MA0153.15.71264e-9
MA0154.10.079
MA0155.10.503
MA0156.12.19603e-8
MA0157.10.0919
MA0159.10.00248
MA0160.10.00441
MA0162.10.132
MA0163.10.00224
MA0164.10.933
MA0258.10.0366
MA0259.10.841



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: CNhs10487

Novel motifP-value
10.209
100.048
1000.304
1010.485
1020.947
1030.106
1040.97
1050.794
1060.102
1070.264
1080.576
1090.00919
110.0755
1100.0612
1110.196
1120.00875
1130.302
1140.501
1150.688
1160.185
1170.00351
1180.472
1190.372
120.967
1200.908
1210.866
1220.675
1234.6079e-4
1240.0139
1250.158
1260.029
1270.251
1280.0664
1290.749
136.68914e-8
1300.149
1310.66
1320.491
1330.687
1340.0849
1350.197
1360.0284
1370.658
1380.649
1390.45
140.877
1400.0952
1410.822
1420.71
1430.429
1440.795
1455.11567e-4
1460.317
1470.249
1480.946
1490.735
150.282
1500.0334
1510.987
1520.0859
1530.875
1541
1550.215
1560.00884
1570.199
1580.507
1590.555
1600.169
1610.108
1620.507
1630.518
1640.0532
1650.106
1660.822
1670.779
1680.433
1690.0038
170.0463
180.849
190.0855
20.665
200.0202
210.181
220.137
230.973
240.0546
250.81
264.76458e-8
270.417
280.766
290.0262
30.0658
300.696
310.783
320.643
330.164
340.829
350.756
360.194
370.024
380.651
390.289
40.224
400.105
410.66
420.216
430.142
440.655
450.771
460.144
470.478
480.363
490.196
50.234
500.195
510.798
520.345
530.327
540.998
550.76
560.537
570.73
580.445
590.126
60.877
600.0549
610.0383
620.358
630.21
640.735
650.584
660.742
670.905
680.976
690.39
70.0235
700.142
710.00469
720.46
730.0217
740.845
750.0444
760.324
770.314
780.00111
790.768
80.0623
800.196
810.657
820.27
830.159
840.992
850.319
860.211
870.12
880.482
890.908
90.545
900.163
910.101
920.212
930.433
940.841
950.0198
960.388
970.928
980.769
990.456



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: CNhs10487


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)
0000955 (brain)
0000369 (corpus striatum)
0002435 (striatum)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0010011 (collection of basal ganglia)
0000204 (ventral part of telencephalon)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011288 (mouse corpus striatum- 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:0010082 (future corpus striatum)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)

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