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|rna_sample_type=
|rna_sample_type=
|rna_extraction_protocol=
|rna_extraction_protocol=
|rna_weight_ug=10.00000
|rna_weight_ug=10
|rna_concentration=0.58000
|rna_concentration=0.58
|sample_note=
|sample_note=
|profile_hcage=CNhs12614,LSID952,release012,COMPLETED
|profile_hcage=CNhs12614,LSID952,release012,COMPLETED

Revision as of 17:49, 27 February 2012


Name:Mouse Neurons - substantia nigra, donor5
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
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 numberRNASUB1
catalog numbercustom
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs12614

00
10.694
100
1000
1000-0.0355
1001-0.0305
1002-0.032
1003-0.0249
10040
10050
10060.687
1007-0.114
10080
1009-0.19
101-0.174
10100
10110.304
10120
10130.355
10140.0653
10150.0246
1016-0.0127
10170
10180
10190
1020
10200.387
10210
10220.2
10230
10240
1025-0.0611
10260
10270.533
10280
1029-0.176
103-0.0665
10300
1031-0.27
10320.465
10330
10340
10350
1036-0.184
10370
1038-0.105
10390.183
1040
1040-0.278
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: CNhs12614

Jaspar motifP-value
MA0002.20.00537
MA0003.10.435
MA0004.10.487
MA0006.10.161
MA0007.10.292
MA0009.10.846
MA0014.10.867
MA0017.18.3748e-7
MA0018.20.00835
MA0019.10.497
MA0024.10.0109
MA0025.10.00112
MA0027.10.0768
MA0028.10.118
MA0029.10.778
MA0030.10.585
MA0031.10.249
MA0035.20.0213
MA0038.10.877
MA0039.20.0142
MA0040.10.294
MA0041.10.0966
MA0042.10.29
MA0043.10.0835
MA0046.11.477e-10
MA0047.23.39584e-4
MA0048.10.0298
MA0050.17.6571e-6
MA0051.19.39236e-5
MA0052.10.612
MA0055.10.00803
MA0057.10.354
MA0058.10.593
MA0059.10.325
MA0060.10.624
MA0061.10.0137
MA0062.20.00217
MA0065.21.74653e-5
MA0066.10.0807
MA0067.10.368
MA0068.10.531
MA0069.10.0499
MA0070.10.404
MA0071.10.21
MA0072.10.215
MA0073.10.891
MA0074.10.168
MA0076.10.306
MA0077.10.386
MA0078.10.891
MA0079.20.41
MA0080.22.24086e-10
MA0081.10.164
MA0083.14.15671e-4
MA0084.10.273
MA0087.10.132
MA0088.10.336
MA0090.10.228
MA0091.10.121
MA0092.10.136
MA0093.10.539
MA0099.28.06354e-4
MA0100.10.317
MA0101.10.00305
MA0102.20.524
MA0103.10.233
MA0104.20.976
MA0105.10.0111
MA0106.10.055
MA0107.10.00368
MA0108.20.00166
MA0111.10.749
MA0112.20.002
MA0113.10.329
MA0114.14.33709e-6
MA0115.11.02712e-4
MA0116.10.167
MA0117.10.884
MA0119.10.0709
MA0122.10.713
MA0124.10.419
MA0125.10.0356
MA0131.10.546
MA0135.10.371
MA0136.15.3253e-12
MA0137.20.102
MA0138.21.6088e-4
MA0139.10.719
MA0140.12.10689e-4
MA0141.10.0683
MA0142.10.0275
MA0143.10.543
MA0144.10.0309
MA0145.10.0914
MA0146.10.0391
MA0147.10.869
MA0148.10.0012
MA0149.10.465
MA0150.10.238
MA0152.10.162
MA0153.14.75483e-10
MA0154.10.0566
MA0155.10.658
MA0156.12.72807e-9
MA0157.10.409
MA0159.10.04
MA0160.10.0485
MA0162.10.374
MA0163.10.0066
MA0164.10.831
MA0258.10.0376
MA0259.10.895



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: CNhs12614

Novel motifP-value
10.253
100.0705
1000.44
1010.837
1020.659
1030.278
1040.771
1050.489
1060.0163
1070.0631
1080.564
1090.0261
110.186
1100.0556
1110.541
1120.0237
1130.539
1140.623
1150.749
1160.433
1170.00284
1180.578
1190.176
120.945
1200.895
1210.136
1220.722
1230.00123
1240.0775
1250.0952
1260.0445
1270.224
1280.0362
1290.235
133.01285e-8
1300.0778
1310.583
1320.655
1330.791
1340.222
1350.3
1360.265
1370.373
1380.732
1390.508
140.688
1400.2
1410.832
1420.552
1430.662
1440.602
1451.35458e-4
1460.261
1470.189
1480.905
1490.93
150.247
1500.0655
1510.977
1520.113
1530.552
1540.727
1550.417
1560.0641
1570.0858
1580.0748
1590.0871
1600.343
1610.26
1620.675
1630.663
1640.0329
1650.275
1660.396
1670.378
1680.97
1690.00231
170.0595
180.729
190.0852
20.64
200.0233
210.267
220.134
230.469
240.0839
250.82
261.77003e-9
270.3
280.72
290.0182
30.127
300.824
310.56
320.907
330.159
340.847
350.463
360.52
370.0329
380.379
390.243
40.303
400.245
410.653
420.207
430.0991
440.857
450.636
460.0558
470.521
480.354
490.169
50.156
500.18
510.829
520.272
530.433
540.785
550.746
560.562
570.663
580.366
590.268
60.869
600.0213
610.048
620.24
630.141
640.769
650.301
660.837
670.749
680.961
690.693
70.0144
700.312
710.00249
720.608
730.0432
740.985
750.0607
760.43
770.468
783.77131e-4
790.054
80.135
800.982
810.659
820.368
830.128
840.894
850.14
860.14
870.97
880.451
890.709
90.306
900.227
910.0848
920.648
930.0175
940.779
950.0503
960.262
970.86
980.588
990.544



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: CNhs12614


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000031 (neuroblast)
0000034 (stem cell)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000117 (CNS neuron (sensu Vertebrata))
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000337 (neuroblast (sensu Vertebrata))
0000393 (electrically responsive cell)
0000404 (electrically signaling cell)
0000540 (neuron)
0000548 (animal cell)
0000723 (somatic stem cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002614 (neuron of the substantia nigra)

UBERON: Anatomy
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000125 (neural nucleus)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001890 (forebrain)
0001891 (midbrain)
0001893 (telencephalon)
0002020 (gray matter)
0002038 (substantia nigra)
0002050 (embryonic structure)
0002298 (brainstem)
0002308 (nucleus of brain)
0002346 (neurectoderm)
0002420 (basal ganglion)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0002950 (regional part of midbrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003528 (brain grey matter)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006331 (brainstem nucleus)
0006598 (presumptive structure)
0007135 (neural keel)
0007284 (presumptive neural plate)

FF: FANTOM5
NA

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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