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|library_id=CNhs12108
 
|library_id=CNhs12108
 
|library_id_phase_based=2:CNhs12108
 
|library_id_phase_based=2:CNhs12108
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11636
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11636
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor3.CNhs12108.11636-122C7.mm10.nobarcode.bam
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor3.CNhs12108.11636-122C7.mm10.nobarcode.bam
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor3.CNhs12108.11636-122C7.mm10.nobarcode.ctss.bed.gz
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor3.CNhs12108.11636-122C7.mm10.nobarcode.ctss.bed.gz

Revision as of 12:10, 18 May 2017


Name:Mouse Granule cells, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12108
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexNA
ageNA
cell typeneuron, granule cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMG1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004673
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12108 CAGE DRX008822 DRR009694
Accession ID Mm9

Library idBAMCTSS
CNhs12108 DRZ001119 DRZ002504
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

CNhs12108

00
10.356
100
1000.441
10000
1001-0.0749
10020.00879
1003-0.102
10040
1005-0.0389
10060.243
1007-0.09
10080
1009-0.19
101-0.233
10100
10110.355
10120
10130.0793
10140
10150.367
10160.315
10170
10180
10190
1020
10200.826
10210
1022-0.0704
10230
1024-0.205
1025-0.0611
10260
10270.213
10280
1029-0.176
103-0.0754
10300
1031-0.333
1032-0.0798
10330.032
10340
10350
1036-0.183
10370
10380.0249
1039-0.138
1040
1040-0.121
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: CNhs12108

Jaspar motifP-value
MA0002.20.00637
MA0003.10.204
MA0004.10.678
MA0006.10.0807
MA0007.10.106
MA0009.10.769
MA0014.10.472
MA0017.13.68511e-5
MA0018.20.013
MA0019.10.345
MA0024.10.987
MA0025.10.833
MA0027.10.833
MA0028.10.227
MA0029.10.857
MA0030.10.476
MA0031.10.0963
MA0035.20.228
MA0038.10.511
MA0039.20.0184
MA0040.10.777
MA0041.10.216
MA0042.10.454
MA0043.10.117
MA0046.11.39928e-6
MA0047.20.00242
MA0048.10.22
MA0050.11.53129e-11
MA0051.11.01478e-5
MA0052.10.0981
MA0055.10.322
MA0057.10.117
MA0058.10.65
MA0059.10.463
MA0060.10.00366
MA0061.10.0478
MA0062.20.0175
MA0065.29.21863e-5
MA0066.10.22
MA0067.10.935
MA0068.10.991
MA0069.10.113
MA0070.10.182
MA0071.10.309
MA0072.10.297
MA0073.10.821
MA0074.10.37
MA0076.10.704
MA0077.10.00163
MA0078.10.0256
MA0079.20.689
MA0080.26.44829e-10
MA0081.10.302
MA0083.10.0199
MA0084.10.549
MA0087.10.592
MA0088.10.113
MA0090.10.0226
MA0091.10.286
MA0092.10.197
MA0093.10.683
MA0099.22.34104e-4
MA0100.10.668
MA0101.10.0272
MA0102.20.411
MA0103.10.255
MA0104.20.583
MA0105.10.0386
MA0106.10.0529
MA0107.10.0262
MA0108.20.647
MA0111.10.861
MA0112.21.52346e-4
MA0113.10.214
MA0114.11.18299e-4
MA0115.10.0289
MA0116.10.0922
MA0117.10.7
MA0119.10.0951
MA0122.10.754
MA0124.10.892
MA0125.10.159
MA0131.10.943
MA0135.10.143
MA0136.11.63631e-9
MA0137.20.00255
MA0138.20.124
MA0139.10.402
MA0140.10.00655
MA0141.10.0153
MA0142.10.00324
MA0143.10.00259
MA0144.10.0086
MA0145.10.0702
MA0146.10.047
MA0147.10.654
MA0148.15.61224e-6
MA0149.10.109
MA0150.10.027
MA0152.10.0665
MA0153.17.41492e-6
MA0154.10.0163
MA0155.10.784
MA0156.12.16272e-7
MA0157.10.0504
MA0159.10.00641
MA0160.10.0769
MA0162.10.328
MA0163.10.00721
MA0164.10.832
MA0258.10.01
MA0259.10.515



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: CNhs12108

Novel motifP-value
10.147
100.0984
1000.656
1010.91
1020.997
1030.0516
1040.953
1050.277
1060.0104
1070.0598
1080.425
1090.00571
110.106
1100.061
1110.0548
1120.00285
1130.924
1140.368
1150.583
1160.638
1170.017
1180.6
1190.134
120.634
1200.749
1210.322
1220.541
1230.0899
1240.554
1250.361
1260.322
1270.0888
1280.0518
1290.186
134.49477e-6
1300.233
1310.435
1320.763
1330.602
1340.464
1350.738
1360.321
1370.197
1380.565
1390.141
140.671
1400.0135
1410.239
1420.00826
1430.962
1440.911
1450.0114
1460.461
1470.769
1480.801
1490.344
150.127
1500.138
1510.49
1520.0507
1530.555
1540.581
1550.645
1560.0127
1570.0555
1580.124
1590.0361
1600.29
1610.328
1620.681
1630.437
1640.00561
1650.0622
1660.507
1670.912
1680.77
1690.00368
170.0114
180.511
190.0692
20.859
200.341
210.595
220.116
230.314
240.0342
250.663
269.6553e-5
270.918
280.318
290.0846
30.0602
300.849
310.896
320.56
330.143
340.675
350.479
360.35
370.0102
380.345
390.2
40.618
400.357
410.967
420.196
430.142
440.874
450.622
460.102
470.295
480.154
490.171
50.163
500.228
510.55
520.117
530.655
540.778
550.73
560.382
570.835
580.203
590.0964
60.705
600.00878
610.168
620.116
630.109
640.787
650.331
660.691
670.908
680.108
690.757
70.0195
700.035
710.00972
720.376
730.0219
740.618
750.0749
760.683
770.242
780.0144
790.548
80.138
800.975
810.577
820.155
830.358
840.738
850.0928
860.225
870.309
880.193
890.321
90.409
900.077
910.538
920.295
930.0153
940.833
950.0446
960.318
970.96
980.987
990.348



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: CNhs12108


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)
0000120 (granule cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000108 (mouse granule cell 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)