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|library_id=CNhs12643
 
|library_id=CNhs12643
 
|library_id_phase_based=2:CNhs12643
 
|library_id_phase_based=2:CNhs12643
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11770
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11770
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor6.CNhs12643.11770-123I6.mm10.nobarcode.bam
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor6.CNhs12643.11770-123I6.mm10.nobarcode.bam
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor6.CNhs12643.11770-123I6.mm10.nobarcode.ctss.bed.gz
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor6.CNhs12643.11770-123I6.mm10.nobarcode.ctss.bed.gz

Revision as of 12:25, 18 May 2017


Name:Mouse Neurons - substantia nigra, donor6
Species:Mouse (Mus musculus)
Library ID:CNhs12643
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesubstantia nigra
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companySciencell/3H
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNASUB2
catalog numbercustom
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005278
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12643 CAGE DRX008848 DRR009720
Accession ID Mm9

Library idBAMCTSS
CNhs12643 DRZ001145 DRZ002530
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

CNhs12643

00
10.712
100
1000
10000
10010.0932
10020
10030.118
10040
10050
10060.566
1007-0.0812
10080
1009-0.128
101-0.138
10100
10110.311
10120.164
10130.186
10140.152
1015-0.0629
1016-0.056
10170
10180
10190
1020
10200.574
10210.0131
10220.0688
10230
10240
10256.239854e-4
10260
10270.427
10280
1029-0.013
103-0.0709
10300
1031-0.374
10320.52
10330.0406
10340
10350
1036-0.183
10370
1038-0.04
10390.134
1040
1040-0.258
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: CNhs12643

Jaspar motifP-value
MA0002.29.93509e-4
MA0003.10.328
MA0004.10.523
MA0006.10.185
MA0007.10.36
MA0009.10.912
MA0014.10.774
MA0017.14.82693e-7
MA0018.20.0315
MA0019.10.521
MA0024.10.0599
MA0025.10.00715
MA0027.10.0473
MA0028.10.0628
MA0029.11
MA0030.10.943
MA0031.10.189
MA0035.20.00967
MA0038.10.831
MA0039.20.0151
MA0040.10.25
MA0041.10.0938
MA0042.10.248
MA0043.10.189
MA0046.16.41334e-11
MA0047.26.07714e-4
MA0048.10.0442
MA0050.17.23053e-5
MA0051.17.21684e-4
MA0052.10.131
MA0055.10.0136
MA0057.10.278
MA0058.10.556
MA0059.10.263
MA0060.10.604
MA0061.10.0246
MA0062.23.65343e-4
MA0065.27.15793e-6
MA0066.10.0469
MA0067.10.348
MA0068.10.654
MA0069.10.108
MA0070.10.499
MA0071.10.088
MA0072.10.294
MA0073.10.926
MA0074.10.135
MA0076.10.151
MA0077.10.278
MA0078.10.802
MA0079.20.362
MA0080.21.06297e-10
MA0081.10.114
MA0083.10.00183
MA0084.10.568
MA0087.10.102
MA0088.10.272
MA0090.10.141
MA0091.10.137
MA0092.10.131
MA0093.10.592
MA0099.25.54619e-4
MA0100.10.232
MA0101.10.0103
MA0102.20.636
MA0103.10.183
MA0104.20.855
MA0105.10.00752
MA0106.10.0675
MA0107.10.0228
MA0108.20.00125
MA0111.10.95
MA0112.25.79976e-4
MA0113.10.254
MA0114.15.57156e-6
MA0115.19.06248e-5
MA0116.10.0911
MA0117.10.926
MA0119.10.109
MA0122.10.805
MA0124.10.602
MA0125.10.0357
MA0131.10.651
MA0135.10.856
MA0136.19.89907e-14
MA0137.20.0805
MA0138.29.90491e-4
MA0139.10.586
MA0140.11.25481e-4
MA0141.10.0119
MA0142.10.404
MA0143.10.879
MA0144.10.0545
MA0145.10.0874
MA0146.10.0367
MA0147.10.734
MA0148.15.12605e-4
MA0149.10.323
MA0150.10.14
MA0152.10.132
MA0153.13.81474e-12
MA0154.10.0467
MA0155.10.526
MA0156.15.23522e-10
MA0157.10.157
MA0159.10.00777
MA0160.10.0166
MA0162.10.241
MA0163.10.00347
MA0164.10.888
MA0258.10.0152
MA0259.10.835



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: CNhs12643

Novel motifP-value
10.206
100.0606
1000.337
1010.991
1020.915
1030.115
1040.882
1050.358
1060.0466
1070.108
1080.499
1090.0124
110.0896
1100.0472
1110.331
1120.0093
1130.664
1140.521
1150.675
1160.435
1170.00299
1180.59
1190.194
120.903
1200.945
1210.18
1220.886
1233.88617e-4
1240.132
1250.155
1260.0504
1270.46
1280.0355
1290.222
138.80261e-8
1300.115
1310.471
1320.491
1330.599
1340.135
1350.369
1360.183
1370.481
1380.873
1390.505
140.936
1400.171
1410.752
1420.641
1430.323
1440.634
1452.94738e-4
1460.23
1470.161
1480.964
1490.703
150.206
1500.0773
1510.881
1520.111
1530.618
1540.652
1550.343
1560.419
1570.101
1580.0954
1590.717
1600.289
1610.176
1620.638
1630.801
1640.0308
1650.276
1660.513
1670.545
1680.533
1690.00218
170.0594
180.813
190.0846
20.707
200.0475
210.229
220.139
230.567
240.069
250.748
262.3136e-8
270.47
280.721
290.0382
30.0909
300.833
310.659
320.821
330.111
340.728
350.714
360.2
370.0371
380.368
390.431
40.261
400.11
410.431
420.186
430.123
440.982
450.665
460.0444
470.379
480.25
490.173
50.191
500.247
510.739
520.319
530.641
540.856
550.907
560.503
570.625
580.291
590.179
60.975
600.0308
610.0548
620.178
630.152
640.67
650.333
660.708
670.817
680.845
690.586
70.0136
700.178
710.00293
720.486
730.0521
740.956
750.0487
760.422
770.529
780.00122
790.0224
80.0819
800.965
810.708
820.264
830.0658
840.865
850.163
860.153
870.282
880.516
890.619
90.345
900.202
910.108
920.413
930.0143
940.65
950.0633
960.208
970.889
980.601
990.491



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: CNhs12643


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002614 (neuron of the substantia nigra)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0002038 (substantia nigra)
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)
0009663 (telencephalic nucleus)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0009661 (midbrain nucleus)
0000125 (neural nucleus)
0002950 (regional part of midbrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0002308 (nucleus of brain)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0001891 (midbrain)
0010011 (collection of basal ganglia)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000208 (mouse neuron of the substantia nigra 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
CL:0000133 (neurectodermal cell)
CL:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)