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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000483,UBERON:0000956,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:0002780,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0001016,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0005743,UBERON:0003075,UBERON:0003056,UBERON:0001049,UBERON:0006238,UBERON:0006601,UBERON:0005068,UBERON:0006241,UBERON:0003080,UBERON:0006240,UBERON:0007284,UBERON:0007135
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0000956,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203
|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:0002609,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:0002609
|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:0000204
|comment=Previously: Mouse Neurons - substantia nigra, donor2
|comment=Previously: Mouse Neurons - substantia nigra, donor2
|created_by=
|created_by=

Revision as of 21:54, 4 July 2012


Name:Mouse Neurons - cortical, donor2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecortex
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 numberRNAMNC3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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

CNhs11947

00
10.224
100
1000.833
10000
1001-0.0749
10020.536
10030.853
10040.055
1005-0.194
10060.104
1007-0.00389
10080
1009-0.19
101-0.135
10100
10110.264
10120.0498
1013-0.2
10140.055
10150.405
10160.233
10170
10180
10190
1020
10200.672
10210.099
1022-0.124
10230
1024-0.14
10250
10260
10270.555
10280
1029-0.122
103-0.0754
10300
1031-0.432
1032-0.177
10330.101
10340
10350
1036-0.0795
10370
10380.0822
1039-0.219
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 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: CNhs11947

Jaspar motifP-value
MA0002.20.00369
MA0003.10.109
MA0004.10.839
MA0006.10.0836
MA0007.10.284
MA0009.10.719
MA0014.10.356
MA0017.15.90785e-6
MA0018.20.128
MA0019.10.316
MA0024.10.108
MA0025.10.209
MA0027.10.692
MA0028.10.788
MA0029.10.614
MA0030.10.293
MA0031.10.0552
MA0035.20.0266
MA0038.10.455
MA0039.20.00321
MA0040.10.648
MA0041.10.398
MA0042.10.939
MA0043.10.123
MA0046.17.96103e-12
MA0047.21.44571e-4
MA0048.10.958
MA0050.13.22891e-9
MA0051.16.34719e-4
MA0052.12.91227e-4
MA0055.10.731
MA0057.10.084
MA0058.10.687
MA0059.10.984
MA0060.14.07196e-4
MA0061.10.0588
MA0062.20.226
MA0065.21.18573e-5
MA0066.10.286
MA0067.10.935
MA0068.10.155
MA0069.10.0718
MA0070.10.477
MA0071.10.25
MA0072.10.113
MA0073.10.825
MA0074.10.404
MA0076.10.642
MA0077.10.00191
MA0078.10.00551
MA0079.20.717
MA0080.23.43002e-11
MA0081.10.376
MA0083.11.15086e-5
MA0084.10.544
MA0087.10.914
MA0088.10.305
MA0090.10.0218
MA0091.10.596
MA0092.10.38
MA0093.10.805
MA0099.21.35285e-5
MA0100.10.827
MA0101.10.13
MA0102.20.745
MA0103.10.0794
MA0104.20.366
MA0105.10.103
MA0106.10.206
MA0107.10.0522
MA0108.21.40306e-4
MA0111.10.78
MA0112.22.2457e-4
MA0113.10.705
MA0114.11.94333e-5
MA0115.10.032
MA0116.10.171
MA0117.10.754
MA0119.10.245
MA0122.10.93
MA0124.10.978
MA0125.10.768
MA0131.10.801
MA0135.10.893
MA0136.13.94315e-9
MA0137.20.0378
MA0138.20.99
MA0139.10.194
MA0140.10.00298
MA0141.10.019
MA0142.10.0116
MA0143.10.00276
MA0144.10.0229
MA0145.10.0235
MA0146.10.0754
MA0147.10.34
MA0148.11.06741e-6
MA0149.10.0693
MA0150.10.0163
MA0152.10.231
MA0153.11.27667e-10
MA0154.10.0281
MA0155.10.721
MA0156.11.41388e-6
MA0157.10.0205
MA0159.10.00406
MA0160.10.077
MA0162.10.391
MA0163.10.0107
MA0164.10.957
MA0258.10.0131
MA0259.10.334



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: CNhs11947

Novel motifP-value
10.257
100.256
1000.897
1010.781
1020.741
1030.183
1040.795
1050.347
1060.00914
1070.0289
1080.44
1090.00412
110.152
1100.189
1110.0856
1120.0048
1130.865
1140.522
1150.211
1160.657
1170.171
1180.746
1190.171
120.448
1200.796
1210.132
1220.332
1230.716
1240.519
1250.328
1260.183
1270.109
1280.04
1290.174
131.04088e-5
1300.746
1310.556
1320.98
1330.49
1340.595
1350.287
1360.103
1370.239
1380.662
1390.313
140.585
1400.902
1410.0776
1420.086
1430.925
1440.834
1450.0814
1460.281
1470.997
1480.917
1490.0978
150.244
1500.29
1510.334
1520.0341
1530.689
1540.97
1550.871
1560.00419
1570.121
1580.112
1590.0146
1600.359
1610.26
1620.991
1630.0397
1640.0172
1650.0109
1660.607
1670.647
1680.356
1690.00691
170.0355
180.592
190.0376
20.489
200.895
210.761
220.0721
230.262
240.0346
250.64
260.0101
270.791
280.282
290.309
30.113
300.396
310.925
320.416
330.239
340.552
350.428
360.732
370.0058
380.44
390.246
40.533
400.189
410.824
420.369
430.186
440.796
450.411
460.266
470.277
480.233
490.22
50.192
500.313
510.669
520.0675
530.477
540.654
550.78
560.361
570.914
580.219
590.0972
60.765
600.00915
610.339
620.137
630.186
640.94
650.49
660.872
670.715
680.813
690.465
70.0225
700.0478
710.0414
720.334
730.0137
740.604
750.141
760.85
770.174
780.0412
790.996
80.367
800.615
810.321
820.0839
830.115
840.642
850.0761
860.252
870.248
880.499
890.206
90.351
900.353
910.555
920.119
930.0169
940.563
950.0473
960.259
970.85
980.637
990.275



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: CNhs11947


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)
0002609 (neuron of cerebral cortex)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0000956 (cerebral cortex)
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)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000204 (cortical mouse 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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