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{{f5samples
{{f5samples
|id=FF:18-22I9
|id=FF:18-22I9
|name=olfactory brain, adult, biol_rep1
|name=olfactory brain, adult
|sample_id=18
|sample_id=18
|rna_tube_id=18-22I9
|rna_tube_id=22I9
|rna_box=18-22I9
|rna_box=22
|rna_position=18-22I9
|rna_position=I9
|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=CNhs10489,LSID647,,COMPLETED
|profile_hcage=CNhs10489,LSID647,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:50, 27 February 2012


Name:olfactory brain, 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
tissueolfactory brain
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]





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

CNhs10489

00
10.707
100
1000
10000
10010.0664
1002-0.0841
10030.128
10040
10050.0504
10060.665
10070.135
10080
1009-0.0442
101-0.0689
10100
10110.591
10120.467
10130.173
10140.0337
10150.0388
1016-0.00757
10170
10180
10190
1020
10200
10210
10220.169
10230
10240
10250
10260
10270.679
10280
10290.11
103-0.0812
10300
1031-0.321
10320.154
10330.0458
10340
10350
1036-0.0428
10370
1038-0.0421
10390.085
1040
1040-0.209
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: CNhs10489

Jaspar motifP-value
MA0002.20.00676
MA0003.10.313
MA0004.10.544
MA0006.10.146
MA0007.10.332
MA0009.10.268
MA0014.10.367
MA0017.11.52118e-6
MA0018.20.00452
MA0019.10.269
MA0024.10.0992
MA0025.10.0456
MA0027.10.0222
MA0028.10.0534
MA0029.10.466
MA0030.10.934
MA0031.10.258
MA0035.20.00309
MA0038.10.209
MA0039.20.00498
MA0040.10.067
MA0041.10.902
MA0042.10.489
MA0043.10.0839
MA0046.12.48476e-12
MA0047.24.7433e-5
MA0048.10.0624
MA0050.10.00729
MA0051.10.0053
MA0052.10.125
MA0055.10.0155
MA0057.10.327
MA0058.10.45
MA0059.10.127
MA0060.10.857
MA0061.10.0462
MA0062.28.30216e-4
MA0065.23.14377e-6
MA0066.10.0439
MA0067.10.71
MA0068.10.934
MA0069.10.0778
MA0070.10.444
MA0071.10.0801
MA0072.10.383
MA0073.10.869
MA0074.10.192
MA0076.10.142
MA0077.10.713
MA0078.10.789
MA0079.20.59
MA0080.22.62196e-9
MA0081.10.345
MA0083.10.087
MA0084.10.994
MA0087.10.53
MA0088.10.422
MA0090.10.112
MA0091.10.139
MA0092.10.147
MA0093.10.596
MA0099.20.00198
MA0100.10.287
MA0101.10.0216
MA0102.20.574
MA0103.10.0939
MA0104.20.878
MA0105.10.0253
MA0106.10.0691
MA0107.10.0605
MA0108.20.00695
MA0111.10.776
MA0112.29.0836e-4
MA0113.10.546
MA0114.17.26552e-6
MA0115.14.12751e-5
MA0116.10.107
MA0117.10.933
MA0119.10.106
MA0122.10.591
MA0124.10.324
MA0125.10.0123
MA0131.10.687
MA0135.10.832
MA0136.11.59926e-13
MA0137.20.322
MA0138.20.00104
MA0139.10.532
MA0140.12.08256e-4
MA0141.10.00112
MA0142.10.188
MA0143.10.69
MA0144.10.0979
MA0145.10.088
MA0146.10.0136
MA0147.10.693
MA0148.11.84511e-4
MA0149.10.127
MA0150.10.155
MA0152.10.96
MA0153.11.93551e-14
MA0154.10.0781
MA0155.10.437
MA0156.12.29021e-8
MA0157.10.259
MA0159.10.0111
MA0160.10.00582
MA0162.10.148
MA0163.10.00244
MA0164.10.88
MA0258.10.018
MA0259.10.863



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: CNhs10489

Novel motifP-value
10.191
100.0573
1000.398
1010.435
1020.861
1030.028
1040.859
1050.507
1060.0705
1070.244
1080.693
1090.00134
110.0504
1100.0628
1110.0685
1120.00545
1130.413
1140.381
1150.778
1160.197
1170.00331
1180.329
1190.236
120.959
1200.969
1210.645
1220.772
1230.0179
1240.0776
1250.388
1260.015
1270.14
1280.0429
1290.59
131.15965e-7
1300.243
1310.623
1320.673
1330.643
1340.0898
1350.657
1360.0459
1370.618
1380.863
1390.302
140.96
1400.0927
1410.759
1420.669
1430.517
1440.457
1450.00223
1460.32
1470.431
1480.77
1490.404
150.171
1500.0951
1510.797
1520.0676
1530.776
1540.908
1550.135
1560.178
1570.323
1580.26
1590.599
1600.247
1610.173
1620.442
1630.842
1640.0349
1650.0206
1660.894
1670.704
1680.631
1690.00443
170.0359
180.723
190.081
20.778
200.0663
210.191
220.136
230.628
240.0385
250.674
261.1672e-6
270.631
280.833
290.0164
30.0722
300.756
310.988
320.377
330.208
340.665
350.711
360.255
370.0236
380.334
390.262
40.22
400.0913
410.468
420.224
430.185
440.159
450.741
460.145
470.304
480.203
490.263
50.228
500.271
510.712
520.307
530.528
540.835
550.854
560.572
570.605
580.317
590.123
60.751
600.049
610.039
620.205
630.152
640.535
650.333
660.734
670.591
680.487
690.429
70.0158
700.0741
710.00522
720.544
730.0185
740.81
750.0361
760.496
770.291
780.00347
790.886
80.0435
800.889
810.841
820.247
830.0213
840.646
850.154
860.215
870.0539
880.488
890.524
90.555
900.095
910.0972
920.239
930.175
940.788
950.0106
960.305
970.857
980.661
990.385



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: CNhs10489


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
0000033 (head)
0000061 (anatomical structure)
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)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)
0007023 (adult organism)

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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