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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000483,UBERON:0000369,UBERON:0002435,UBERON:0000033,UBERON:0000479,UBERON:0002346,UBERON:0000064,UBERON:0000073,UBERON:0004121,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000025,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000477,UBERON:0002020,UBERON:0002791,UBERON:0003528,UBERON:0000481,UBERON:0000467,UBERON:0002616,UBERON:0001062,UBERON:0000119,UBERON:0005291,UBERON:0002420,UBERON:0002780,UBERON:0007245,UBERON:0006598,UBERON:0002532,UBERON:0010009,UBERON:0001017,UBERON:0001016,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0001893,UBERON:0001890,UBERON:0005743,UBERON:0010011,UBERON:0000204,UBERON:0003075,UBERON:0003056,UBERON:0001049,UBERON:0006238,UBERON:0000454,UBERON:0010082,UBERON:0006601,UBERON:0005068,UBERON:0006241,UBERON:0003080,UBERON:0006240,UBERON:0007284,UBERON:0007135
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000540,CL:0000055,CL:0000047,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0002321,CL:0002371,CL:0002319,CL:0000221,CL:0000117,CL:0000393,CL:0000220,CL:0000004,CL:0000031,CL:0000211,CL:0000404,CL:0000255,CL:0002613,CL:0000133,CL:0000337
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0002613
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000203,FF:0000209
|comment=
|comment=
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|created_by=

Revision as of 21:51, 4 July 2012


Name:Mouse Neurons - striatal, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecorpus striatum
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMNS2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
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

CNhs12134

00
10.38
100
1000.412
1000-0.0355
1001-0.0749
1002-0.0618
1003-0.00666
10040.0269
1005-0.166
10060.297
1007-0.0387
10080
1009-0.2
101-0.189
10100
10110.117
10120
1013-0.0029
10140.0143
10150.377
10160.314
10170
10180
10190
1020
10200.646
10210.053
1022-0.0704
10230
1024-0.221
1025-0.016
10260
10270.223
10280
1029-0.148
103-0.0848
10300
1031-0.467
10320.06
10330.0538
10340
10350
1036-0.208
10370
10380.0708
1039-0.219
1040
1040-0.162
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 no result for this sample


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: CNhs12134

Jaspar motifP-value
MA0002.20.00401
MA0003.10.184
MA0004.10.627
MA0006.10.0938
MA0007.10.152
MA0009.10.915
MA0014.10.412
MA0017.14.29699e-5
MA0018.20.0103
MA0019.10.314
MA0024.10.896
MA0025.10.697
MA0027.10.619
MA0028.10.504
MA0029.10.505
MA0030.10.326
MA0031.10.0816
MA0035.20.156
MA0038.10.252
MA0039.20.0235
MA0040.10.785
MA0041.10.23
MA0042.10.561
MA0043.10.0541
MA0046.12.23386e-7
MA0047.20.0022
MA0048.10.346
MA0050.12.95862e-9
MA0051.12.92578e-4
MA0052.10.0985
MA0055.10.362
MA0057.10.0881
MA0058.10.581
MA0059.10.408
MA0060.10.00105
MA0061.10.0474
MA0062.20.146
MA0065.22.791e-5
MA0066.10.147
MA0067.10.888
MA0068.10.821
MA0069.10.0918
MA0070.10.357
MA0071.10.253
MA0072.10.222
MA0073.10.936
MA0074.10.37
MA0076.10.807
MA0077.10.00881
MA0078.10.0557
MA0079.20.622
MA0080.28.0982e-10
MA0081.10.353
MA0083.10.00623
MA0084.10.653
MA0087.10.406
MA0088.10.188
MA0090.10.00821
MA0091.10.216
MA0092.10.135
MA0093.10.632
MA0099.21.66632e-4
MA0100.10.943
MA0101.10.054
MA0102.20.914
MA0103.10.168
MA0104.20.618
MA0105.10.0312
MA0106.10.108
MA0107.10.048
MA0108.20.107
MA0111.10.995
MA0112.21.27478e-4
MA0113.10.236
MA0114.11.1707e-4
MA0115.10.00722
MA0116.10.0636
MA0117.10.738
MA0119.10.0437
MA0122.10.556
MA0124.10.866
MA0125.10.151
MA0131.10.879
MA0135.10.15
MA0136.11.29154e-7
MA0137.20.00749
MA0138.20.224
MA0139.10.261
MA0140.10.00484
MA0141.10.0112
MA0142.10.0218
MA0143.10.00618
MA0144.10.0192
MA0145.10.0565
MA0146.10.0514
MA0147.10.686
MA0148.11.64095e-5
MA0149.10.0816
MA0150.10.0342
MA0152.10.152
MA0153.15.91923e-7
MA0154.10.0154
MA0155.10.639
MA0156.14.83295e-5
MA0157.10.0566
MA0159.10.0034
MA0160.10.0723
MA0162.10.294
MA0163.10.0023
MA0164.10.908
MA0258.10.0121
MA0259.10.554



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: CNhs12134

Novel motifP-value
10.145
100.09
1000.758
1010.977
1020.894
1030.0893
1040.97
1050.155
1060.00713
1070.0454
1080.53
1090.00372
110.0839
1100.0912
1110.0951
1120.00627
1130.962
1140.305
1150.564
1160.492
1170.0474
1180.428
1190.142
120.682
1200.878
1210.448
1220.782
1230.181
1240.642
1250.384
1260.233
1270.134
1280.0216
1290.279
135.77667e-6
1300.359
1310.384
1320.946
1330.231
1340.364
1350.638
1360.204
1370.223
1380.646
1390.105
140.674
1400.0429
1410.261
1420.0179
1430.536
1440.995
1450.0126
1460.406
1470.789
1480.409
1490.116
150.18
1500.132
1510.457
1520.0521
1530.522
1540.703
1550.663
1560.00879
1570.111
1580.22
1590.124
1600.198
1610.444
1620.74
1630.37
1640.0175
1650.0411
1660.69
1670.948
1680.443
1690.00382
170.0216
180.727
190.054
20.913
200.481
210.459
220.0852
230.236
240.0361
250.694
266.93915e-4
270.868
280.379
290.11
30.0712
300.676
310.912
320.385
330.167
340.551
350.505
360.36
370.00999
380.268
390.162
40.56
400.294
410.904
420.223
430.13
440.624
450.517
460.132
470.174
480.116
490.147
50.138
500.234
510.532
520.103
530.681
540.662
550.831
560.391
570.571
580.215
590.0717
60.512
600.0115
610.152
620.114
630.101
640.892
650.226
660.698
670.796
680.281
690.611
70.0167
700.0212
710.0139
720.345
730.026
740.35
750.119
760.709
770.239
780.0152
790.468
80.131
800.864
810.501
820.0862
830.174
840.816
850.0995
860.287
870.316
880.277
890.287
90.317
900.132
910.238
920.288
930.0452
940.765
950.0464
960.344
970.85
980.787
990.321



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: CNhs12134


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)
0002613 (striatum neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0000369 (corpus striatum)
0002435 (striatum)
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)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000209 (mouse striatal neuron 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
NA

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