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{{f5samples
{{f5samples
|id=FF:1396-42A3
|id=FF:1396-42A3
|name=medulla oblongata, neonate N30, biol_rep1
|name=medulla oblongata, neonate N30
|sample_id=1396
|sample_id=1396
|rna_tube_id=1396-42A3
|rna_tube_id=42A3
|rna_box=1396-42A3
|rna_box=42
|rna_position=1396-42A3
|rna_position=A3
|sample_cell_lot=
|sample_cell_lot=
|sample_cell_catalog=
|sample_cell_catalog=
Line 32: Line 32:
|rna_concentration=
|rna_concentration=
|sample_note=
|sample_note=
|profile_hcage=CNhs11200,LSID747,,COMPLETED
|profile_hcage=CNhs11200,LSID747,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:46, 27 February 2012


Name:medulla oblongata, neonate N30
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuemedulla oblongata
dev stage30 days neonate
sexmixture
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]





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

CNhs11200

00
10.718
100
1000
10000.0343
10010.1
1002-0.0161
10030.0268
10040.0241
10050.00926
10060.6
1007-0.0214
10080
1009-0.152
101-0.0749
10100
10110.287
10120.131
10130.328
1014-0.037
1015-0.184
1016-0.0983
10170
10180
10190
1020
10200
10210
10220.0857
10230
10240.17
10250
10260
10270.464
10280
10290.0527
103-0.0799
10300
1031-0.317
10320.46
1033-0.0142
10340
10350.0481
1036-0.233
10370
1038-0.0942
10390.116
1040
1040-0.168
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: CNhs11200

Jaspar motifP-value
MA0002.22.7993e-4
MA0003.10.291
MA0004.10.437
MA0006.10.259
MA0007.10.379
MA0009.10.879
MA0014.10.854
MA0017.12.63946e-6
MA0018.20.00504
MA0019.10.447
MA0024.10.0638
MA0025.10.00179
MA0027.10.224
MA0028.10.125
MA0029.10.911
MA0030.10.604
MA0031.10.417
MA0035.20.0179
MA0038.10.206
MA0039.20.0762
MA0040.10.485
MA0041.10.0489
MA0042.10.151
MA0043.10.0282
MA0046.12.47318e-12
MA0047.21.63525e-4
MA0048.10.0365
MA0050.13.79163e-5
MA0051.15.45499e-4
MA0052.10.357
MA0055.10.0162
MA0057.10.234
MA0058.10.536
MA0059.10.131
MA0060.10.281
MA0061.10.0172
MA0062.20.00506
MA0065.21.58615e-6
MA0066.10.022
MA0067.10.246
MA0068.10.938
MA0069.10.0581
MA0070.10.341
MA0071.10.181
MA0072.10.918
MA0073.10.826
MA0074.10.109
MA0076.10.308
MA0077.10.159
MA0078.10.747
MA0079.20.262
MA0080.21.25764e-9
MA0081.10.208
MA0083.10.014
MA0084.10.657
MA0087.10.0642
MA0088.10.358
MA0090.10.0844
MA0091.10.157
MA0092.10.227
MA0093.10.525
MA0099.20.0105
MA0100.10.19
MA0101.10.0123
MA0102.20.461
MA0103.10.104
MA0104.20.632
MA0105.10.0012
MA0106.10.0618
MA0107.10.024
MA0108.29.57768e-4
MA0111.10.815
MA0112.28.70092e-4
MA0113.10.497
MA0114.16.48243e-6
MA0115.15.76756e-5
MA0116.10.0382
MA0117.10.982
MA0119.10.127
MA0122.10.98
MA0124.10.476
MA0125.10.00717
MA0131.10.802
MA0135.10.368
MA0136.13.77549e-11
MA0137.20.305
MA0138.21.48988e-4
MA0139.10.521
MA0140.11.58628e-5
MA0141.10.0204
MA0142.10.434
MA0143.10.74
MA0144.10.0795
MA0145.10.217
MA0146.10.0528
MA0147.10.435
MA0148.15.51366e-4
MA0149.10.237
MA0150.10.255
MA0152.10.259
MA0153.11.92247e-12
MA0154.10.0235
MA0155.10.454
MA0156.15.23882e-7
MA0157.10.287
MA0159.10.00324
MA0160.10.0279
MA0162.10.265
MA0163.15.39927e-4
MA0164.10.895
MA0258.10.015
MA0259.10.679



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: CNhs11200

Novel motifP-value
10.276
100.0529
1000.357
1010.752
1020.914
1030.0717
1040.948
1050.581
1060.0306
1070.126
1080.591
1090.0181
110.121
1100.0394
1110.2
1120.00867
1130.526
1140.459
1150.782
1160.25
1170.00379
1180.255
1190.215
120.786
1200.646
1210.606
1220.812
1234.86989e-4
1240.0428
1250.215
1260.0274
1270.209
1280.0282
1290.298
136.21618e-7
1300.182
1310.507
1320.67
1330.537
1340.204
1350.14
1360.27
1370.627
1380.853
1390.261
140.741
1400.0969
1410.74
1420.527
1430.326
1440.937
1451.6809e-4
1460.406
1470.364
1480.88
1490.988
150.164
1500.0792
1510.984
1520.156
1530.852
1540.789
1550.475
1560.00763
1570.283
1580.326
1590.617
1600.183
1610.243
1620.864
1630.471
1640.028
1650.517
1660.454
1670.774
1680.496
1690.00356
170.0884
180.935
190.164
20.78
200.0271
210.178
220.207
230.7
240.098
250.718
263.73002e-10
270.45
280.846
290.0272
30.0935
300.906
310.758
320.533
330.179
340.818
350.884
360.163
370.066
380.49
390.415
40.237
400.153
410.442
420.217
430.126
440.494
450.716
460.0249
470.495
480.338
490.167
50.19
500.294
510.724
520.384
530.354
540.924
550.949
560.539
570.473
580.284
590.098
60.88
600.0383
610.0785
620.157
630.168
640.622
650.358
660.818
670.845
680.514
690.606
70.018
700.0922
710.00258
720.586
730.0826
740.906
750.0589
760.256
770.498
780.00266
790.167
80.0519
800.861
810.576
820.305
830.3
840.586
850.239
860.134
870.652
880.596
890.511
90.495
900.208
910.0585
920.279
930.14
940.779
950.12
960.479
970.893
980.452
990.465



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: CNhs11200


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

UBERON: Anatomy
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
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)
0001896 (medulla oblongata)
0002028 (hindbrain)
0002050 (embryonic structure)
0002298 (brainstem)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0003057 (chordal neural plate)
0003075 (neural plate)
0003076 (posterior neural tube)
0004121 (ectoderm-derived structure)
0004732 (segmental subdivision of nervous system)
0004733 (segmental subdivision of hindbrain)
0005068 (neural rod)
0005290 (myelencephalon)
0005423 (developing anatomical structure)
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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