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{{f5samples
{{f5samples
|id=FF:505-44H7
|id=FF:505-44H7
|name=ovary, embryo E18, biol_rep1
|name=ovary, embryo E18
|sample_id=505
|sample_id=505
|rna_tube_id=505-44H7
|rna_tube_id=44H7
|rna_box=505-44H7
|rna_box=44
|rna_position=505-44H7
|rna_position=H7
|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=CNhs11040,LSID732,,COMPLETED
|profile_hcage=CNhs11040,LSID732,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:50, 27 February 2012


Name:ovary, embryo E18
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueovary
dev stage18 days embryo
sexfemale
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

CNhs11040

00
10
100
1000
10000.0569
10010
10020.675
10030.211
10040.68
10050
10060.106
10070.0241
10080
10090.225
101-0.0356
10100
10110.0179
10120
1013-0.146
10140.316
10150.24
10160.382
10170
10180
10190
1020
10200
10210.0225
10220.0028
10230
10240.0798
10250.132
10260.103
10270
10280
1029-0.106
1030.501
10300
10310.733
10320.0286
10330
10340
10350
10360.119
10370
10380.0715
1039-0.0594
1040
10400.241
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: CNhs11040

Jaspar motifP-value
MA0002.20.0619
MA0003.10.296
MA0004.10.997
MA0006.10.99
MA0007.10.771
MA0009.10.487
MA0014.10.748
MA0017.10.0674
MA0018.20.00434
MA0019.10.355
MA0024.11.99906e-5
MA0025.10.182
MA0027.10.129
MA0028.10.115
MA0029.10.406
MA0030.10.0917
MA0031.10.131
MA0035.20.284
MA0038.10.391
MA0039.20.34
MA0040.10.124
MA0041.10.373
MA0042.10.313
MA0043.10.195
MA0046.10.646
MA0047.20.00862
MA0048.10.318
MA0050.10.211
MA0051.10.0627
MA0052.10.0746
MA0055.10.0147
MA0057.10.937
MA0058.10.888
MA0059.10.856
MA0060.10.0011
MA0061.10.879
MA0062.21.47984e-4
MA0065.20.196
MA0066.10.299
MA0067.10.0126
MA0068.10.232
MA0069.10.93
MA0070.10.174
MA0071.10.224
MA0072.10.0397
MA0073.10.95
MA0074.10.214
MA0076.10.273
MA0077.10.635
MA0078.10.0698
MA0079.20.0383
MA0080.24.02079e-6
MA0081.10.116
MA0083.10.00785
MA0084.10.746
MA0087.10.107
MA0088.10.482
MA0090.10.446
MA0091.10.598
MA0092.10.743
MA0093.10.99
MA0099.20.00456
MA0100.10.131
MA0101.10.283
MA0102.20.441
MA0103.10.00322
MA0104.20.851
MA0105.10.638
MA0106.10.285
MA0107.10.213
MA0108.20.00621
MA0111.10.598
MA0112.20.369
MA0113.10.925
MA0114.10.0618
MA0115.10.0116
MA0116.10.508
MA0117.10.00822
MA0119.10.68
MA0122.10.916
MA0124.10.374
MA0125.10.473
MA0131.10.882
MA0135.10.107
MA0136.11.88809e-6
MA0137.20.109
MA0138.20.147
MA0139.10.984
MA0140.10.487
MA0141.10.101
MA0142.10.0182
MA0143.10.556
MA0144.10.23
MA0145.10.869
MA0146.10.223
MA0147.10.723
MA0148.10.0121
MA0149.10.0177
MA0150.14.29206e-5
MA0152.10.0824
MA0153.10.701
MA0154.10.654
MA0155.10.05
MA0156.10.00421
MA0157.10.353
MA0159.10.0178
MA0160.10.0466
MA0162.10.376
MA0163.10.0626
MA0164.10.998
MA0258.10.0166
MA0259.10.559



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: CNhs11040

Novel motifP-value
10.118
100.175
1000.85
1010.668
1020.692
1030.117
1040.535
1050.887
1060.0808
1070.747
1080.752
1090.664
110.488
1100.611
1110.133
1120.91
1130.533
1140.0775
1150.735
1160.397
1170.125
1180.739
1190.103
120.709
1200.366
1210.795
1220.778
1230.0988
1240.312
1250.0359
1260.851
1270.0225
1280.045
1290.271
130.825
1300.438
1310.321
1320.72
1330.86
1340.828
1350.233
1360.0986
1370.659
1380.32
1390.0248
140.307
1400.425
1410.536
1420.122
1430.429
1440.15
1450.829
1460.865
1470.821
1480.574
1490.514
150.0406
1500.491
1510.213
1520.44
1530.357
1540.434
1550.598
1560.175
1570.24
1580.0356
1590.0283
1600.143
1610.718
1620.418
1630.0401
1640.188
1650.201
1660.0509
1670.134
1680.435
1690.238
170.503
180.102
190.157
20.324
200.597
210.521
220.375
230.404
240.72
250.103
260.739
270.839
280.124
290.47
30.533
300.523
310.473
320.283
330.794
340.485
350.0206
360.23
370.554
380.923
390.436
40.528
400.932
410.109
420.765
430.266
440.261
450.577
460.293
470.337
480.367
490.0445
50.238
500.104
510.854
520.989
530.684
540.465
550.569
560.465
570.294
580.273
590.308
60.589
600.499
610.694
620.0652
630.787
640.959
650.533
660.717
670.983
680.273
690.706
70.54
700.0284
710.379
720.672
730.829
740.821
750.44
760.363
770.804
780.175
790.539
80.256
800.128
810.312
820.787
830.432
840.232
850.0514
860.814
870.59
880.664
890.502
90.866
900.0047
910.47
920.291
930.799
940.0598
950.968
960.137
970.904
980.759
990.111



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: CNhs11040


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
0000061 (anatomical structure)
0000062 (organ)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000991 (gonad)
0000992 (female gonad)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0004120 (mesoderm-derived structure)
0004176 (external genitalia)
0004458 (body cavity or lining)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005564 (gonad primordium)
0009117 (indifferent gonad)
0009196 (indifferent external genitalia)

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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