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{{f5samples
{{f5samples
|id=FF:460-26E5
|id=FF:460-26E5
|name=pancreas, embryo E16, biol_rep1
|name=pancreas, embryo E16
|sample_id=460
|sample_id=460
|rna_tube_id=460-26E5
|rna_tube_id=26E5
|rna_box=460-26E5
|rna_box=26
|rna_position=460-26E5
|rna_position=E5
|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=CNhs11003,LSID730,,COMPLETED
|profile_hcage=CNhs11003,LSID730,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:50, 27 February 2012


Name:pancreas, embryo E16
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 stage16 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

CNhs11003

00
10
100
1000
10000.0715
10010
10020.195
1003-0.0468
10040
10050
1006-0.143
10070.0266
10080
1009-0.0572
1010.07
10100.892
1011-0.0628
10120
10130.501
10140.312
1015-0.0645
1016-0.096
10170
10180.139
10190
1020
10200
10210.0263
10220.177
10230
1024-5.586389e-4
10250.134
10260
10270
10280
10290.0188
1030.0875
10300
10310.171
1032-0.0375
10330
10340.244
10350
10360.102
10370
1038-0.0375
10390.012
1040
10400.00266
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: CNhs11003

Jaspar motifP-value
MA0002.20.0146
MA0003.10.662
MA0004.10.0639
MA0006.10.362
MA0007.10.0962
MA0009.10.961
MA0014.10.738
MA0017.10.799
MA0018.24.57239e-4
MA0019.10.955
MA0024.10.04
MA0025.10.0239
MA0027.10.574
MA0028.10.00115
MA0029.10.11
MA0030.10.439
MA0031.10.3
MA0035.20.364
MA0038.10.806
MA0039.20.327
MA0040.10.118
MA0041.10.44
MA0042.10.865
MA0043.10.0201
MA0046.12.03731e-36
MA0047.23.00726e-4
MA0048.10.232
MA0050.11.93795e-4
MA0051.12.58282e-5
MA0052.12.73028e-5
MA0055.10.109
MA0057.10.895
MA0058.10.11
MA0059.12.20403e-5
MA0060.12.83854e-4
MA0061.10.76
MA0062.20.023
MA0065.20.172
MA0066.10.581
MA0067.10.0328
MA0068.10.215
MA0069.10.436
MA0070.10.73
MA0071.10.989
MA0072.10.897
MA0073.10.747
MA0074.10.0656
MA0076.10.017
MA0077.10.325
MA0078.10.98
MA0079.20.499
MA0080.20.00949
MA0081.10.0931
MA0083.10.0179
MA0084.10.499
MA0087.10.966
MA0088.10.0123
MA0090.10.723
MA0091.12.65379e-8
MA0092.10.314
MA0093.10.0544
MA0099.20.00196
MA0100.10.0132
MA0101.10.826
MA0102.20.0402
MA0103.11.16253e-6
MA0104.20.0364
MA0105.10.0945
MA0106.10.295
MA0107.10.183
MA0108.20.0477
MA0111.10.447
MA0112.20.00799
MA0113.10.247
MA0114.10.738
MA0115.10.897
MA0116.10.168
MA0117.10.865
MA0119.10.0187
MA0122.10.375
MA0124.10.813
MA0125.10.723
MA0131.10.148
MA0135.10.888
MA0136.10.00369
MA0137.20.0228
MA0138.20.0962
MA0139.10.046
MA0140.10.0513
MA0141.10.0384
MA0142.10.193
MA0143.10.395
MA0144.10.169
MA0145.10.273
MA0146.10.421
MA0147.10.00316
MA0148.12.39256e-4
MA0149.10.333
MA0150.10.146
MA0152.10.966
MA0153.11.47398e-15
MA0154.10.0743
MA0155.10.235
MA0156.10.47
MA0157.10.944
MA0159.10.213
MA0160.10.487
MA0162.10.329
MA0163.14.73432e-4
MA0164.10.211
MA0258.10.144
MA0259.10.0303



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: CNhs11003

Novel motifP-value
10.231
100.0703
1000.205
1010.609
1020.603
1030.151
1040.825
1050.665
1060.392
1070.45
1080.882
1090.00265
110.294
1100.0586
1110.155
1120.172
1130.0213
1140.627
1150.807
1160.122
1170.0712
1180.966
1190.974
120.399
1200.611
1210.125
1220.327
1230.0627
1240.232
1250.552
1260.0101
1270.633
1280.502
1290.194
134.09986e-5
1300.65
1310.756
1320.705
1330.56
1340.104
1350.888
1360.0488
1370.806
1380.0142
1390.97
140.506
1400.204
1410.345
1420.725
1430.987
1440.208
1450.0502
1460.772
1470.225
1480.281
1490.364
150.247
1500.442
1510.768
1520.125
1530.683
1540.93
1550.88
1560.0134
1570.706
1580.734
1590.683
1600.0335
1610.118
1620.452
1630.202
1640.405
1650.691
1660.396
1670.711
1680.719
1690.113
170.468
180.468
190.0849
20.372
200.381
210.558
220.523
230.303
240.0258
250.924
265.6035e-4
270.863
280.202
290.0971
30.474
300.907
310.519
320.739
330.303
340.477
350.876
360.148
370.0544
380.978
390.248
40.352
400.291
410.0757
420.262
430.973
440.129
450.692
460.327
470.865
480.651
490.589
50.829
500.37
510.775
520.933
530.799
540.344
550.818
560.682
570.741
580.555
590.469
60.957
600.539
610.164
620.829
630.291
640.609
650.518
660.1
670.889
680.0219
690.984
70.0965
700.545
710.0014
720.837
730.065
740.64
750.141
760.648
770.323
780.355
790.158
80.101
800.133
810.176
820.332
830.919
840.0395
850.826
860.306
870.493
880.903
890.778
90.86
900.353
910.987
920.622
930.883
940.342
950.0439
960.906
970.335
980.567
990.669



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: CNhs11003


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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