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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0000955,UBERON:0001894,UBERON:0000483,UBERON:0000033,UBERON:0000479,UBERON:0002346,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: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:0001890,UBERON:0005743,UBERON:0003075,UBERON:0003056,UBERON:0001049,UBERON:0006238,UBERON:0006601,UBERON:0005068,UBERON:0006241,UBERON:0003080,UBERON:0006240,UBERON:0006222,UBERON:0007284,UBERON:0007135
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|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000101,FF:0000001,FF:0000998,FF:0000004,FF:0010193
|comment=
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Revision as of 00:36, 5 July 2012


Name:diencephalon, adult
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuediencephalon
dev stageadult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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

CNhs10482

00
10.771
100
1000
10000
10010.124
1002-0.0751
10030.132
10040.082
10050.0345
10060.579
1007-0.103
10080
1009-0.19
101-0.0855
10100
10110.549
10120.151
10130.272
1014-0.0851
1015-0.0251
1016-0.00199
10170
10180
10190
1020
10200
10210
10220.0347
10230
10240.0114
10250
10260
10270.425
10280
10290.0344
103-0.0861
10300.082
1031-0.336
10320.395
1033-0.0665
10340
10350
1036-0.133
10370
1038-0.0167
10390.129
1040
1040-0.189
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: CNhs10482

Jaspar motifP-value
MA0002.20.00127
MA0003.10.341
MA0004.10.466
MA0006.10.195
MA0007.10.297
MA0009.10.754
MA0014.10.744
MA0017.11.60245e-6
MA0018.20.00956
MA0019.10.617
MA0024.10.0519
MA0025.10.00199
MA0027.10.0852
MA0028.10.0554
MA0029.10.896
MA0030.10.842
MA0031.10.287
MA0035.20.0206
MA0038.10.599
MA0039.20.0341
MA0040.10.39
MA0041.10.0369
MA0042.10.252
MA0043.10.0792
MA0046.11.97573e-10
MA0047.27.2676e-4
MA0048.10.0226
MA0050.14.72246e-5
MA0051.10.00274
MA0052.10.741
MA0055.10.00489
MA0057.10.334
MA0058.10.488
MA0059.10.158
MA0060.10.84
MA0061.10.0263
MA0062.25.19664e-4
MA0065.21.69034e-6
MA0066.10.049
MA0067.10.489
MA0068.10.625
MA0069.10.0504
MA0070.10.493
MA0071.10.147
MA0072.10.809
MA0073.10.981
MA0074.10.178
MA0076.10.134
MA0077.10.416
MA0078.10.891
MA0079.20.327
MA0080.25.88263e-10
MA0081.10.27
MA0083.10.00883
MA0084.10.815
MA0087.10.138
MA0088.10.233
MA0090.10.125
MA0091.10.188
MA0092.10.142
MA0093.10.527
MA0099.20.00499
MA0100.10.253
MA0101.10.0107
MA0102.20.482
MA0103.10.211
MA0104.20.804
MA0105.10.0056
MA0106.10.0354
MA0107.10.0259
MA0108.20.0017
MA0111.10.944
MA0112.28.2926e-4
MA0113.10.515
MA0114.16.47116e-6
MA0115.11.60724e-5
MA0116.10.0922
MA0117.10.934
MA0119.10.153
MA0122.10.702
MA0124.10.379
MA0125.10.0304
MA0131.10.642
MA0135.10.352
MA0136.11.76918e-12
MA0137.20.182
MA0138.22.3374e-5
MA0139.10.639
MA0140.16.45205e-5
MA0141.10.00946
MA0142.10.162
MA0143.10.654
MA0144.10.0721
MA0145.10.162
MA0146.10.0344
MA0147.10.647
MA0148.17.7385e-4
MA0149.10.0797
MA0150.10.271
MA0152.10.156
MA0153.12.11423e-10
MA0154.10.0526
MA0155.10.401
MA0156.11.65051e-8
MA0157.10.129
MA0159.10.00323
MA0160.10.0148
MA0162.10.207
MA0163.14.89598e-4
MA0164.10.871
MA0258.10.0189
MA0259.10.767



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: CNhs10482

Novel motifP-value
10.207
100.0395
1000.342
1010.757
1020.984
1030.0761
1040.873
1050.551
1060.0575
1070.158
1080.528
1090.0141
110.0926
1100.0469
1110.234
1120.00717
1130.473
1140.444
1150.889
1160.221
1170.00294
1180.359
1190.218
120.997
1200.838
1210.72
1220.638
1235.5466e-4
1240.038
1250.197
1260.0317
1270.222
1280.0528
1290.343
138.83796e-8
1300.226
1310.546
1320.748
1330.613
1340.0915
1350.117
1360.0788
1370.797
1380.892
1390.239
140.805
1400.0713
1410.97
1420.817
1430.299
1440.706
1451.5917e-4
1460.351
1470.25
1480.878
1490.971
150.205
1500.0639
1510.988
1520.137
1530.796
1540.788
1550.318
1560.00597
1570.127
1580.31
1590.937
1600.206
1610.149
1620.649
1630.69
1640.0382
1650.219
1660.598
1670.686
1680.573
1690.00302
170.0709
180.919
190.114
20.63
200.0214
210.192
220.167
230.78
240.0657
250.729
262.05798e-8
270.398
280.795
290.0307
30.069
300.738
310.666
320.597
330.154
340.757
350.699
360.179
370.0327
380.495
390.348
40.222
400.0896
410.523
420.161
430.122
440.502
450.78
460.0817
470.464
480.325
490.176
50.156
500.271
510.795
520.396
530.386
540.959
550.807
560.554
570.478
580.331
590.143
60.894
600.058
610.0452
620.233
630.201
640.76
650.445
660.951
670.856
680.465
690.502
70.0177
700.128
710.00258
720.502
730.0517
740.996
750.0484
760.315
770.489
780.00195
790.318
80.0599
800.62
810.769
820.333
830.245
840.849
850.321
860.145
870.334
880.516
890.803
90.519
900.126
910.0939
920.329
930.164
940.814
950.0519
960.301
970.971
980.752
990.505



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: CNhs10482


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000955 (brain)
0001894 (diencephalon)
0000479 (tissue)
0004121 (ectoderm-derived structure)
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)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001890 (forebrain)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0010193 (human diencephalon - adult 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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