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{{f5samples
{{f5samples
|id=FF:405-44F4
|id=FF:405-44F4
|name=pancreas, embryo E14, biol_rep1
|name=pancreas, embryo E14
|sample_id=405
|sample_id=405
|rna_tube_id=405-44F4
|rna_tube_id=44F4
|rna_box=405-44F4
|rna_box=44
|rna_position=405-44F4
|rna_position=F4
|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=CNhs11012,LSID730,,COMPLETED
|profile_hcage=CNhs11012,LSID730,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:50, 27 February 2012


Name:pancreas, embryo E14
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepancreas
dev stage14 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

CNhs11012

00
10
100
1000
10000.0117
10010.00785
10020.491
1003-0.0469
10040
10050
1006-0.143
1007-3.128138e-4
10080
1009-0.0281
1010.102
10100.768
1011-0.0131
10120.0944
1013-0.126
10140.643
10150.167
10160.0893
10170
10180
10190
1020
10200
10210.0163
1022-0.0632
10230
10240.082
10250.233
10260
10270.0334
10280
1029-0.00496
1030.172
10300
10310.206
1032-0.0822
10330.0967
10340.0322
10350
10360.208
10370
1038-0.0941
1039-0.0117
1040
10400.0791
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: CNhs11012

Jaspar motifP-value
MA0002.22.91802e-4
MA0003.10.749
MA0004.10.399
MA0006.10.897
MA0007.10.44
MA0009.10.842
MA0014.10.611
MA0017.10.0467
MA0018.20.0304
MA0019.10.689
MA0024.15.47639e-10
MA0025.10.0123
MA0027.10.06
MA0028.10.00165
MA0029.10.303
MA0030.10.0277
MA0031.10.00594
MA0035.20.774
MA0038.10.442
MA0039.20.412
MA0040.10.0925
MA0041.10.21
MA0042.10.315
MA0043.10.6
MA0046.13.48631e-25
MA0047.20.621
MA0048.10.0488
MA0050.12.72432e-7
MA0051.11.30669e-7
MA0052.16.27851e-7
MA0055.10.00122
MA0057.10.417
MA0058.10.282
MA0059.11.79057e-4
MA0060.15.51113e-8
MA0061.10.731
MA0062.20.0308
MA0065.20.486
MA0066.10.583
MA0067.10.0131
MA0068.10.682
MA0069.10.365
MA0070.10.248
MA0071.10.222
MA0072.10.0224
MA0073.10.892
MA0074.10.163
MA0076.10.0127
MA0077.10.459
MA0078.10.909
MA0079.20.298
MA0080.22.0505e-6
MA0081.10.0951
MA0083.10.166
MA0084.10.658
MA0087.10.61
MA0088.10.285
MA0090.10.498
MA0091.10.0111
MA0092.10.802
MA0093.10.392
MA0099.21.72416e-5
MA0100.10.528
MA0101.10.532
MA0102.20.0471
MA0103.10.182
MA0104.20.031
MA0105.10.166
MA0106.10.71
MA0107.10.115
MA0108.20.451
MA0111.10.461
MA0112.20.754
MA0113.10.777
MA0114.10.0509
MA0115.10.422
MA0116.10.519
MA0117.10.0213
MA0119.10.902
MA0122.10.157
MA0124.10.465
MA0125.10.748
MA0131.10.0818
MA0135.10.632
MA0136.17.54696e-4
MA0137.20.425
MA0138.20.00365
MA0139.10.46
MA0140.10.0911
MA0141.10.32
MA0142.10.353
MA0143.10.476
MA0144.10.71
MA0145.10.733
MA0146.10.611
MA0147.10.00196
MA0148.10.681
MA0149.10.587
MA0150.14.72773e-4
MA0152.10.999
MA0153.11.39388e-13
MA0154.10.819
MA0155.10.169
MA0156.10.13
MA0157.10.0267
MA0159.10.586
MA0160.10.121
MA0162.10.307
MA0163.10.00448
MA0164.10.418
MA0258.10.298
MA0259.10.216



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: CNhs11012

Novel motifP-value
10.362
100.311
1000.395
1010.502
1020.676
1030.616
1040.974
1050.242
1060.126
1070.0515
1080.976
1090.472
110.738
1100.405
1110.184
1120.39
1130.0589
1140.00586
1150.536
1160.69
1170.254
1180.521
1190.204
120.462
1200.854
1210.834
1220.712
1230.0577
1240.0832
1250.204
1260.349
1270.335
1280.228
1290.0108
130.0319
1300.335
1310.956
1320.631
1330.86
1340.0943
1350.416
1360.374
1370.934
1380.219
1390.0371
140.276
1400.633
1410.495
1420.664
1430.701
1440.37
1450.774
1460.425
1470.538
1480.581
1490.823
150.162
1500.915
1510.0298
1520.734
1530.638
1540.484
1550.577
1562.38952e-5
1570.896
1580.809
1590.598
1600.344
1610.428
1620.351
1630.0592
1640.743
1650.493
1660.382
1670.971
1680.915
1690.745
170.352
180.608
190.492
20.26
200.39
210.46
220.949
230.00829
240.656
250.432
260.0583
270.31
280.0427
290.415
30.949
300.758
310.663
320.664
330.6
340.975
350.37
360.344
370.826
380.709
390.518
40.544
400.303
410.0521
420.594
430.155
440.979
450.424
460.833
470.721
480.713
490.173
50.0905
500.506
510.469
520.493
530.345
540.184
550.665
560.933
570.923
580.441
590.551
60.209
600.421
610.482
620.176
630.44
640.967
650.663
660.207
670.768
680.479
690.807
70.69
700.00591
710.288
720.288
730.425
740.161
750.806
760.301
770.538
780.227
790.852
80.31
800.167
810.207
820.453
830.543
840.0858
850.0387
860.986
870.503
880.844
890.307
90.486
900.907
910.623
920.351
930.696
940.169
950.31
960.6
970.896
980.647
990.261



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: CNhs11012


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)
0000077 (mixed endoderm/mesoderm-derived structure)
0000160 (intestine)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial 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)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001045 (midgut)
0001048 (primordium)
0001062 (anatomical entity)
0001264 (pancreas)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002108 (small intestine)
0002114 (duodenum)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003921 (pancreas primordium)
0003922 (pancreatic epithelial bud)
0003923 (dorsal pancreatic bud)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004921 (subdivision of digestive tract)
0005177 (trunk region element)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

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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