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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008696
|DRA_sample_Accession=CAGE@SAMD00005734
|accession_numbers=CAGE;DRX008806;DRR009678;DRZ001103;DRZ002488
|accession_numbers=CAGE;DRX008806;DRR009678;DRZ001103;DRZ002488
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0002037,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002680,UBERON:0002616,UBERON:0004733,UBERON:0004732,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001895,UBERON:0002028
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0002037,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002680,UBERON:0002616,UBERON:0004733,UBERON:0004732,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001895,UBERON:0002028

Revision as of 20:19, 31 July 2014


Name:Mouse Astrocytes - cerebellar, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs13077
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecerebellum
dev stageNA
sexNA
ageNA
cell typeastrocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNA3928
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005734
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13077 CAGE DRX008806 DRR009678
Accession ID Mm9

Library idBAMCTSS
CNhs13077 DRZ001103 DRZ002488
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

CNhs13077

00
10
100
1000
10000.142
1001-0.0749
10020
10030.438
10040.205
10050
10060.078
1007-0.427
10080
10090.209
101-0.533
10100
10110.0731
10120
10130.204
10140.0202
10150.197
10160.311
10170
10180
10190
1020
10200.409
10210.251
1022-0.131
10230
1024-0.151
10250
10260
1027-0.048
10280
1029-0.176
1030.527
10300
10311.046
10320.341
10330
10340
10350
10360.0682
10370
1038-0.0473
1039-0.118
1040
10400.626
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: CNhs13077

Jaspar motifP-value
MA0002.20.357
MA0003.10.374
MA0004.10.563
MA0006.10.276
MA0007.10.0504
MA0009.10.265
MA0014.10.397
MA0017.10.146
MA0018.20.439
MA0019.10.204
MA0024.10.0414
MA0025.10.687
MA0027.10.287
MA0028.10.0793
MA0029.10.827
MA0030.10.619
MA0031.10.65
MA0035.20.0864
MA0038.10.00769
MA0039.20.264
MA0040.10.684
MA0041.10.278
MA0042.10.722
MA0043.10.756
MA0046.12.70179e-4
MA0047.20.377
MA0048.10.373
MA0050.10.305
MA0051.10.704
MA0052.10.0612
MA0055.10.0153
MA0057.10.487
MA0058.10.421
MA0059.10.731
MA0060.10.153
MA0061.10.271
MA0062.20.0151
MA0065.20.595
MA0066.10.905
MA0067.10.0234
MA0068.10.693
MA0069.10.444
MA0070.10.409
MA0071.10.733
MA0072.10.656
MA0073.10.691
MA0074.10.0469
MA0076.10.081
MA0077.10.0812
MA0078.10.761
MA0079.20.0171
MA0080.20.0556
MA0081.10.794
MA0083.10.00154
MA0084.10.741
MA0087.10.5
MA0088.10.492
MA0090.10.00271
MA0091.10.339
MA0092.10.357
MA0093.10.559
MA0099.20.124
MA0100.10.212
MA0101.10.603
MA0102.20.884
MA0103.16.18838e-4
MA0104.20.581
MA0105.10.41
MA0106.10.0309
MA0107.10.823
MA0108.20.706
MA0111.10.978
MA0112.20.178
MA0113.10.119
MA0114.10.295
MA0115.10.2
MA0116.10.196
MA0117.10.361
MA0119.10.296
MA0122.10.579
MA0124.10.252
MA0125.10.267
MA0131.10.177
MA0135.10.0319
MA0136.10.0324
MA0137.20.701
MA0138.20.118
MA0139.10.701
MA0140.10.00423
MA0141.10.575
MA0142.10.26
MA0143.10.93
MA0144.10.915
MA0145.10.04
MA0146.10.00473
MA0147.10.592
MA0148.10.146
MA0149.10.852
MA0150.10.404
MA0152.10.303
MA0153.11.47923e-4
MA0154.10.219
MA0155.10.244
MA0156.10.0035
MA0157.10.735
MA0159.10.56
MA0160.10.638
MA0162.10.188
MA0163.10.0467
MA0164.10.85
MA0258.10.61
MA0259.10.347



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: CNhs13077

Novel motifP-value
10.424
100.704
1000.194
1010.586
1020.151
1030.536
1040.592
1050.466
1060.0759
1070.752
1080.439
1090.00779
110.173
1100.5
1110.569
1120.602
1130.287
1140.874
1150.831
1160.0272
1170.59
1180.609
1190.615
120.795
1200.596
1210.815
1220.445
1230.527
1240.128
1250.407
1260.572
1270.596
1280.439
1290.718
130.623
1300.596
1310.665
1320.51
1330.683
1340.91
1350.791
1360.0235
1370.13
1380.982
1390.0478
140.9
1400.272
1410.619
1420.142
1430.173
1440.495
1450.577
1460.523
1470.43
1480.801
1490.0757
150.662
1500.0895
1510.924
1520.00664
1530.22
1540.119
1550.318
1560.0485
1570.635
1580.082
1590.283
1600.876
1610.384
1620.716
1630.714
1640.113
1650.481
1660.783
1670.0122
1680.852
1690.0819
170.282
180.508
190.227
20.0568
200.859
210.263
220.0313
230.582
240.237
250.0381
260.816
270.98
280.484
290.659
30.757
300.281
310.953
320.0437
330.982
340.158
350.684
360.237
370.0844
380.308
390.466
40.676
400.428
410.692
420.698
430.253
440.506
450.271
460.956
470.409
480.738
490.551
50.0787
500.0367
510.497
520.223
530.956
540.436
550.674
560.289
570.956
580.14
590.018
60.731
600.231
610.65
620.318
630.171
640.35
650.071
660.28
670.861
680.614
690.249
70.249
700.62
710.575
720.833
730.00123
740.652
750.564
760.523
770.0268
780.93
790.681
80.926
800.0989
810.419
820.808
830.494
840.817
850.155
860.712
870.00461
880.698
890.301
90.947
900.513
910.469
920.717
930.343
940.183
950.058
960.0848
970.559
980.238
990.776



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: CNhs13077


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)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000128 (oligodendrocyte)
0000126 (macroglial cell)
0000125 (glial cell)
0000255 (eukaryotic cell)
0000127 (astrocyte)
0002603 (astrocyte of the cerebellum)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0002037 (cerebellum)
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)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002680 (regional part of metencephalon)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001895 (metencephalon)
0002028 (hindbrain)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000105 (mouse astrocyte sample)
0000196 (mouse astrocyte of cerebellum 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:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)

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