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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000160,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001045,UBERON:0001048,UBERON:0001062,UBERON:0001264,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002100,UBERON:0002108,UBERON:0002114,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003104,UBERON:0003921,UBERON:0003922,UBERON:0003923,UBERON:0003924,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004458,UBERON:0004921,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002108,UBERON:0001264,UBERON:0002100,UBERON:0000160,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000077,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004921,UBERON:0005423,UBERON:0002553,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0002323,UBERON:0005177,UBERON:0003104,UBERON:0000464,UBERON:0004458,UBERON:0001048,UBERON:0000925,UBERON:0006598,UBERON:0003886,UBERON:0003922,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0002114,UBERON:0005409,UBERON:0007026,UBERON:0001041,UBERON:0000949,UBERON:0009142,UBERON:0003923,UBERON:0006595,UBERON:0006603,UBERON:0001045,UBERON:0003924,UBERON:0003921
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=

Revision as of 18:17, 8 June 2012


Name:pancreas, 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
tissuepancreas
dev stage18 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]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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

CNhs10580

00
10
100
1000
10000.0325
10010.0307
10020.115
1003-0.087
10040
10050
1006-0.0262
1007-0.0184
10080
10090.148
1010.033
10100.348
1011-0.101
10120
10130.529
10140.261
1015-0.0194
1016-0.061
10170
10180.0567
10190
1020
10200
10210.116
10220.327
10230
10240.116
10250.287
10260
10270.0554
10280
1029-0.0604
1030.147
10300
10310.296
10320.1
10330.116
10340.368
10350
1036-0.0224
10370
10380.0319
10390.0159
1040
10400.0939
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: CNhs10580

Jaspar motifP-value
MA0002.20.388
MA0003.10.319
MA0004.10.0973
MA0006.10.175
MA0007.10.165
MA0009.10.688
MA0014.10.539
MA0017.10.337
MA0018.20.226
MA0019.10.904
MA0024.10.893
MA0025.10.785
MA0027.10.845
MA0028.10.9
MA0029.10.243
MA0030.10.576
MA0031.10.54
MA0035.20.0552
MA0038.10.286
MA0039.20.00365
MA0040.10.773
MA0041.10.243
MA0042.10.69
MA0043.10.597
MA0046.12.80267e-34
MA0047.22.9963e-5
MA0048.10.769
MA0050.10.585
MA0051.10.393
MA0052.10.0104
MA0055.10.271
MA0057.10.663
MA0058.10.146
MA0059.10.0618
MA0060.14.38341e-5
MA0061.10.859
MA0062.20.633
MA0065.20.57
MA0066.10.872
MA0067.10.0865
MA0068.10.443
MA0069.10.476
MA0070.10.304
MA0071.10.151
MA0072.10.532
MA0073.10.697
MA0074.10.0344
MA0076.10.906
MA0077.10.727
MA0078.10.957
MA0079.20.0604
MA0080.20.476
MA0081.10.462
MA0083.10.907
MA0084.10.943
MA0087.10.391
MA0088.10.0718
MA0090.10.0628
MA0091.11.8934e-4
MA0092.10.403
MA0093.10.0964
MA0099.20.0791
MA0100.10.00139
MA0101.10.753
MA0102.20.312
MA0103.17.33688e-6
MA0104.20.41
MA0105.10.655
MA0106.10.865
MA0107.10.375
MA0108.20.359
MA0111.10.287
MA0112.20.427
MA0113.10.616
MA0114.10.156
MA0115.10.345
MA0116.10.487
MA0117.10.828
MA0119.10.225
MA0122.10.494
MA0124.10.875
MA0125.10.737
MA0131.10.503
MA0135.10.0298
MA0136.10.095
MA0137.20.00351
MA0138.20.154
MA0139.10.137
MA0140.10.0817
MA0141.10.844
MA0142.10.224
MA0143.10.351
MA0144.10.021
MA0145.10.027
MA0146.10.209
MA0147.10.198
MA0148.11.68419e-6
MA0149.10.352
MA0150.10.063
MA0152.10.927
MA0153.11.69796e-15
MA0154.10.119
MA0155.10.121
MA0156.10.991
MA0157.10.245
MA0159.10.871
MA0160.10.427
MA0162.10.554
MA0163.10.417
MA0164.10.0197
MA0258.10.919
MA0259.10.199



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: CNhs10580

Novel motifP-value
10.853
100.488
1000.775
1010.32
1020.717
1030.854
1040.267
1050.837
1060.427
1070.61
1080.863
1090.0387
110.772
1100.354
1110.689
1120.882
1130.0689
1140.0529
1150.86
1160.538
1170.893
1180.122
1190.816
120.167
1200.621
1210.178
1220.475
1230.433
1240.355
1250.134
1260.0679
1270.882
1280.462
1290.846
130.00689
1300.836
1310.137
1320.865
1330.582
1340.114
1350.506
1360.0125
1370.0929
1380.0181
1390.465
140.849
1400.497
1410.901
1420.45
1430.903
1440.14
1450.622
1460.316
1470.204
1480.178
1490.356
150.163
1500.645
1510.322
1520.0149
1530.76
1540.132
1550.978
1560.00241
1570.643
1580.709
1590.789
1600.171
1610.197
1620.574
1630.967
1640.7
1650.811
1660.0726
1670.36
1680.683
1690.144
170.324
180.0618
190.0743
20.303
200.735
210.572
220.266
230.935
240.0486
250.388
260.0576
270.974
280.129
290.743
30.489
300.287
310.779
320.761
330.225
340.656
350.0564
360.864
370.262
380.896
390.374
40.237
400.249
410.096
420.825
430.584
440.966
450.462
460.677
470.918
480.979
490.291
50.216
500.239
510.985
520.371
530.391
540.561
550.874
560.406
570.0616
580.814
590.0693
60.465
600.249
610.339
620.326
630.411
640.953
650.367
660.0534
670.85
680.0473
690.908
70.329
700.156
710.454
720.446
730.0587
740.802
750.971
760.21
770.0736
780.73
790.11
80.908
800.171
810.0716
820.986
830.886
840.0778
850.826
860.424
870.0366
880.255
890.71
90.664
900.466
910.968
920.372
930.957
940.0247
950.301
960.123
970.0395
980.43
990.304



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: CNhs10580


FANTOM5 (FF) ontology

Direct parent terms


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
0000468 (multi-cellular organism)
0000922 (embryo)
0002108 (small intestine)
0001264 (pancreas)
0002100 (trunk)
0000160 (intestine)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0000077 (mixed endoderm/mesoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0002553 (anatomical cavity)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0005291 (embryonic tissue)
0002323 (body cavity)
0005177 (trunk region element)
0003104 (mesenchyme)
0000464 (anatomical space)
0004458 (body cavity or lining)
0001048 (primordium)
0000925 (endoderm)
0006598 (presumptive structure)
0003886 (body cavity precursor)
0003922 (pancreatic epithelial bud)
0004185 (endodermal part of digestive tract)
0002532 (epiblast (generic))
0001555 (digestive tract)
0002114 (duodenum)
0005409 (gastrointestinal system)
0007026 (primitive gut)
0001041 (foregut)
0000949 (endocrine system)
0009142 (entire embryonic mesenchyme)
0003923 (dorsal pancreatic bud)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0001045 (midgut)
0003921 (pancreas primordium)

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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