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{{f5samples
{{f5samples
|id=FF:346-16E6
|id=FF:346-16E6
|name=pituitary gland, embryo E12, biol_rep1
|name=pituitary gland, embryo E12
|sample_id=346
|sample_id=346
|rna_tube_id=346-16E6
|rna_tube_id=16E6
|rna_box=346-16E6
|rna_box=16
|rna_position=346-16E6
|rna_position=E6
|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=CNhs11018,LSID731,,COMPLETED
|profile_hcage=CNhs11018,LSID731,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:50, 27 February 2012


Name:pituitary gland, embryo E12
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepituitary gland
dev stage12 days embryo
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

CNhs11018

00
10.0537
100
1000.116
1000-0.0355
10010
10020.353
1003-0.102
10040.418
1005-0.0967
1006-0.0538
10070.17
10080
1009-0.0241
1010.0875
10100
10110.0204
10120
1013-0.203
10140.318
10150.318
10160.167
10170
10180
10190
1020
10200
10210.0232
10220
10230
1024-0.0607
10250.134
10260
10270.229
10280
1029-0.014
1030
10300
10310.238
1032-0.0878
10330.024
10340
10350
10360.109
10370
1038-0.0194
1039-0.123
1040
10400.0199
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: CNhs11018

Jaspar motifP-value
MA0002.22.48882e-5
MA0003.10.12
MA0004.10.768
MA0006.10.372
MA0007.10.364
MA0009.10.368
MA0014.10.402
MA0017.11.3671e-5
MA0018.20.187
MA0019.10.823
MA0024.19.89778e-4
MA0025.10.00292
MA0027.10.202
MA0028.10.239
MA0029.10.384
MA0030.10.174
MA0031.10.00677
MA0035.20.00937
MA0038.10.00386
MA0039.20.0358
MA0040.10.0706
MA0041.10.24
MA0042.10.444
MA0043.10.0362
MA0046.11.89899e-26
MA0047.24.2476e-5
MA0048.10.293
MA0050.11.64522e-5
MA0051.14.90417e-4
MA0052.13.67965e-8
MA0055.10.145
MA0057.10.0276
MA0058.10.793
MA0059.10.809
MA0060.17.18174e-16
MA0061.10.0402
MA0062.20.546
MA0065.22.25613e-5
MA0066.10.0518
MA0067.10.366
MA0068.10.237
MA0069.10.327
MA0070.10.653
MA0071.10.16
MA0072.10.0979
MA0073.10.667
MA0074.10.534
MA0076.10.128
MA0077.10.0419
MA0078.10.41
MA0079.20.943
MA0080.21.16685e-10
MA0081.10.244
MA0083.10.0349
MA0084.10.704
MA0087.10.139
MA0088.10.478
MA0090.10.233
MA0091.10.58
MA0092.10.272
MA0093.10.819
MA0099.21.43858e-6
MA0100.10.668
MA0101.10.244
MA0102.20.609
MA0103.10.0351
MA0104.20.76
MA0105.10.00817
MA0106.10.214
MA0107.10.114
MA0108.20.944
MA0111.10.51
MA0112.26.38339e-7
MA0113.10.43
MA0114.11.87445e-4
MA0115.10.0199
MA0116.10.0119
MA0117.10.553
MA0119.10.00473
MA0122.10.755
MA0124.10.4
MA0125.10.00315
MA0131.10.389
MA0135.10.942
MA0136.11.95343e-6
MA0137.20.294
MA0138.20.00196
MA0139.10.0526
MA0140.10.0507
MA0141.10.00389
MA0142.10.186
MA0143.10.00538
MA0144.10.193
MA0145.10.0127
MA0146.10.233
MA0147.10.855
MA0148.11.42278e-5
MA0149.10.011
MA0150.10.00529
MA0152.10.1
MA0153.19.98276e-18
MA0154.19.94653e-4
MA0155.10.602
MA0156.10.0242
MA0157.10.0556
MA0159.10.0125
MA0160.10.0142
MA0162.10.53
MA0163.10.0143
MA0164.10.669
MA0258.11.39695e-4
MA0259.10.733



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: CNhs11018

Novel motifP-value
10.0845
100.266
1000.76
1010.653
1020.859
1030.0917
1040.631
1050.12
1060.00973
1070.0922
1080.717
1090.134
110.0995
1100.167
1110.00907
1120.0234
1130.45
1140.0448
1150.856
1160.476
1170.393
1180.945
1190.0962
120.898
1200.608
1210.7
1220.922
1230.279
1240.196
1250.395
1260.448
1270.032
1280.0412
1290.188
130.0997
1300.474
1310.163
1320.442
1330.494
1340.706
1350.0978
1360.983
1370.722
1380.549
1390.0162
140.337
1400.00611
1410.0744
1420.461
1430.425
1440.971
1450.196
1460.327
1470.702
1480.244
1490.147
150.0983
1500.535
1510.135
1520.0444
1530.655
1540.599
1550.613
1560.9
1570.982
1580.392
1590.495
1600.571
1610.832
1620.565
1630.0917
1640.138
1650.123
1660.773
1670.934
1680.15
1690.0011
170.0697
180.502
190.135
20.404
200.551
210.977
220.206
230.0597
240.431
250.447
260.154
270.395
280.471
290.463
30.177
300.657
310.576
320.0868
330.611
340.661
350.503
360.357
370.0461
380.2
390.61
40.386
400.319
410.345
420.511
430.129
440.108
450.405
460.196
470.135
480.114
490.133
50.138
500.907
510.523
520.26
530.563
540.473
550.603
560.386
570.456
580.277
590.0374
60.647
600.0663
610.865
620.0944
630.102
640.48
650.0896
660.439
670.654
680.147
690.363
70.165
709.87886e-4
710.128
720.329
730.0673
740.51
750.234
760.663
770.138
780.0859
790.185
80.24
800.182
810.325
820.0566
830.505
840.5
850.0163
860.366
870.603
880.765
890.126
90.339
900.25
910.362
920.0892
930.191
940.423
950.174
960.208
970.699
980.238
990.693



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: CNhs11018


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
0000007 (pituitary gland)
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
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)
0000949 (endocrine system)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001890 (forebrain)
0001894 (diencephalon)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003296 (gland of diencephalon)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
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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