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{{f5samples
{{f5samples
|id=FF:34-16E4
|id=FF:34-16E4
|name=pancreas, adult, biol_rep1
|name=pancreas, adult
|sample_id=34
|sample_id=34
|rna_tube_id=34-16E4
|rna_tube_id=16E4
|rna_box=34-16E4
|rna_box=16
|rna_position=34-16E4
|rna_position=E4
|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=CNhs10486,LSID647,,COMPLETED
|profile_hcage=CNhs10486,LSID647,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:50, 27 February 2012


Name:pancreas, 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
tissuepancreas
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

CNhs10486

00
10
100
1000
10000
1001-0.0275
1002-0.0468
10030.00645
10040
1005-0.0372
1006-0.0359
1007-0.0264
10080
1009-0.0572
101-0.0417
10100
1011-0.298
10120
10130.699
1014-0.0851
1015-0.315
1016-0.453
10170
10180
10190
1020
10200
10210
10220.957
10230
10240.0598
10250
10260
10270
10280
1029-0.176
103-0.0719
10300
1031-0.495
1032-0.11
1033-0.0752
10341.206
10350
10360.00746
10370
10380.0167
10390.26
1040
1040-0.0865
10410.367



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: CNhs10486

Jaspar motifP-value
MA0002.20.037
MA0003.10.381
MA0004.10.235
MA0006.10.341
MA0007.10.194
MA0009.10.815
MA0014.10.391
MA0017.10.129
MA0018.20.0204
MA0019.10.902
MA0024.11.2182e-4
MA0025.10.816
MA0027.10.993
MA0028.10.338
MA0029.10.748
MA0030.10.926
MA0031.10.312
MA0035.20.0138
MA0038.10.019
MA0039.20.687
MA0040.10.771
MA0041.10.144
MA0042.10.509
MA0043.10.0354
MA0046.11.83062e-8
MA0047.27.3634e-4
MA0048.10.415
MA0050.10.874
MA0051.10.726
MA0052.15.15674e-4
MA0055.10.395
MA0057.10.4
MA0058.10.309
MA0059.10.0137
MA0060.11.90313e-8
MA0061.10.677
MA0062.20.534
MA0065.20.00487
MA0066.10.456
MA0067.10.35
MA0068.10.0877
MA0069.10.443
MA0070.10.72
MA0071.10.109
MA0072.10.0444
MA0073.10.628
MA0074.10.107
MA0076.10.399
MA0077.10.75
MA0078.10.246
MA0079.20.514
MA0080.20.679
MA0081.10.455
MA0083.10.00197
MA0084.10.724
MA0087.10.0797
MA0088.10.101
MA0090.10.306
MA0091.10.00139
MA0092.10.406
MA0093.10.244
MA0099.20.762
MA0100.10.192
MA0101.10.826
MA0102.20.192
MA0103.17.75027e-6
MA0104.20.195
MA0105.10.281
MA0106.10.159
MA0107.10.691
MA0108.20.00394
MA0111.10.687
MA0112.22.61834e-5
MA0113.10.401
MA0114.10.331
MA0115.10.504
MA0116.10.365
MA0117.10.332
MA0119.10.494
MA0122.10.38
MA0124.10.284
MA0125.10.86
MA0131.10.406
MA0135.10.891
MA0136.10.448
MA0137.20.0272
MA0138.20.51
MA0139.10.249
MA0140.10.0381
MA0141.10.00533
MA0142.10.0759
MA0143.10.867
MA0144.10.0982
MA0145.10.0394
MA0146.10.113
MA0147.10.0701
MA0148.11.16122e-5
MA0149.10.0225
MA0150.10.275
MA0152.10.836
MA0153.10.00438
MA0154.10.019
MA0155.10.388
MA0156.10.81
MA0157.10.145
MA0159.10.0186
MA0160.10.0221
MA0162.10.258
MA0163.10.00214
MA0164.10.447
MA0258.10.00599
MA0259.10.924



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: CNhs10486

Novel motifP-value
10.0447
100.139
1000.458
1010.769
1020.87
1030.0466
1040.35
1050.963
1060.0474
1070.255
1080.973
1090.0679
110.111
1100.0527
1110.00188
1120.0451
1130.623
1140.0569
1150.574
1160.515
1170.241
1180.98
1190.035
120.851
1200.476
1210.657
1220.228
1230.716
1240.809
1250.156
1260.193
1270.362
1280.0286
1290.0687
130.0732
1300.561
1310.68
1320.651
1330.25
1340.75
1350.825
1360.736
1370.226
1380.354
1390.0257
140.759
1400.0201
1410.45
1420.401
1430.546
1440.284
1450.0972
1460.254
1470.927
1480.149
1490.434
150.228
1500.363
1510.358
1520.0445
1530.523
1540.999
1550.116
1560.224
1570.495
1580.157
1590.548
1600.249
1610.369
1620.703
1630.525
1640.108
1650.152
1660.506
1670.528
1680.901
1690.0121
170.132
180.471
190.104
20.354
200.947
210.992
220.337
230.352
240.211
250.624
260.0535
270.332
280.563
290.458
30.259
300.998
310.328
320.38
330.843
340.861
350.122
360.111
370.0349
380.378
390.618
40.103
400.472
410.447
420.273
430.211
440.119
450.613
460.102
470.253
480.252
490.117
50.305
500.99
510.67
520.543
530.923
540.627
550.315
560.31
570.7
580.216
590.035
60.61
600.122
610.226
620.152
630.158
640.374
650.0802
660.598
670.437
680.204
690.33
70.123
700.011
710.0415
720.373
730.0444
740.541
750.185
760.85
770.0972
780.125
790.00625
80.0963
800.769
810.255
820.0513
830.576
840.622
850.0214
860.0265
870.179
880.477
890.264
90.734
900.079
910.311
920.109
930.132
940.724
950.696
960.353
970.00542
980.355
990.399



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: CNhs10486


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)
0007023 (adult organism)
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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