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|name=Ileum epithelium, pool1
|name=Ileum epithelium, pool1
|sample_id=10252
|sample_id=10252
|rna_tube_id=
|rna_tube_id=104B9
|rna_box=104
|rna_box=104
|rna_position=B9
|rna_position=B9
Line 20: Line 20:
|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=2.14000
|rna_od260/230=2.14
|rna_od260/280=2.17000
|rna_od260/280=2.17
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_cell_line=
Line 29: Line 29:
|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=1.37390
|rna_weight_ug=1.3739
|rna_concentration=
|rna_concentration=0.1249
|sample_note=
|sample_note=
|profile_hcage=CNhs13199,LSID1004,,MAPPING
|profile_hcage=CNhs13199,LSID1004,release012,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:39, 27 February 2012


Name:Ileum epithelium, pool1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/c
tissueileum
dev stageNA
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberCont_ileum_a
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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

CNhs13199

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.107
1003-0.123
10040
10050.328
1006-0.183
1007-0.201
10082.597
1009-0.19
101-0.203
10100
1011-0.262
10120
10130.369
1014-0.0874
1015-0.327
1016-0.589
10170
10180.401
10190
1020
10200.0756
10210.221
1022-0.124
10230
1024-0.307
10250
10260
1027-0.048
10280
1029-0.1
103-0.0887
10300
1031-0.911
10320.768
1033-0.0713
10340.0433
10350
1036-0.184
10370
10380.0794
10390.0446
1040.0756
1040-0.216
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: CNhs13199

Jaspar motifP-value
MA0002.20.0159
MA0003.10.226
MA0004.10.765
MA0006.10.105
MA0007.10.212
MA0009.10.21
MA0014.10.0751
MA0017.14.25996e-24
MA0018.20.0429
MA0019.10.479
MA0024.10.0582
MA0025.10.1
MA0027.10.569
MA0028.10.0318
MA0029.10.428
MA0030.10.93
MA0031.10.624
MA0035.28.83498e-4
MA0038.10.406
MA0039.26.50169e-4
MA0040.10.0251
MA0041.10.346
MA0042.10.582
MA0043.10.00359
MA0046.17.98585e-48
MA0047.20.0148
MA0048.10.436
MA0050.11.05993e-4
MA0051.12.81571e-5
MA0052.13.66086e-4
MA0055.10.578
MA0057.10.0943
MA0058.10.775
MA0059.10.494
MA0060.10.0131
MA0061.10.335
MA0062.25.11138e-4
MA0065.26.81693e-13
MA0066.10.0947
MA0067.10.354
MA0068.10.0602
MA0069.10.417
MA0070.10.0421
MA0071.10.0927
MA0072.10.961
MA0073.10.638
MA0074.10.179
MA0076.10.0746
MA0077.10.503
MA0078.10.93
MA0079.20.288
MA0080.21.04047e-4
MA0081.10.839
MA0083.10.00502
MA0084.10.32
MA0087.10.598
MA0088.10.236
MA0090.10.791
MA0091.10.906
MA0092.10.688
MA0093.10.83
MA0099.27.30199e-5
MA0100.10.856
MA0101.10.509
MA0102.20.273
MA0103.13.9961e-7
MA0104.20.559
MA0105.10.141
MA0106.10.339
MA0107.10.679
MA0108.20.146
MA0111.10.971
MA0112.25.96042e-5
MA0113.10.453
MA0114.16.9978e-25
MA0115.15.71046e-13
MA0116.10.163
MA0117.10.609
MA0119.10.0587
MA0122.10.707
MA0124.10.167
MA0125.10.618
MA0131.10.957
MA0135.10.494
MA0136.11.74432e-8
MA0137.20.0712
MA0138.20.581
MA0139.10.0465
MA0140.10.0584
MA0141.13.22529e-7
MA0142.10.171
MA0143.10.0745
MA0144.10.0122
MA0145.10.0217
MA0146.10.205
MA0147.10.696
MA0148.10.00396
MA0149.10.00466
MA0150.10.0836
MA0152.10.0291
MA0153.13.0645e-42
MA0154.10.0836
MA0155.10.809
MA0156.17.23276e-5
MA0157.10.945
MA0159.11.89953e-4
MA0160.17.24291e-4
MA0162.10.403
MA0163.10.02
MA0164.10.67
MA0258.10.0143
MA0259.10.742



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: CNhs13199

Novel motifP-value
10.0934
100.0734
1000.616
1010.831
1020.74
1030.15
1040.866
1050.474
1060.0655
1070.258
1080.76
1090.0412
110.112
1100.145
1110.123
1120.0226
1130.488
1140.017
1150.603
1160.12
1170.0296
1180.393
1190.105
120.569
1200.308
1210.665
1220.927
1230.0861
1240.278
1250.211
1260.0508
1270.276
1280.184
1290.161
131.50135e-4
1300.646
1310.603
1320.537
1330.962
1340.876
1350.107
1360.0238
1370.528
1380.205
1390.0489
140.726
1400.0923
1410.0692
1420.842
1430.457
1440.25
1450.0914
1460.362
1470.963
1480.44
1490.795
150.148
1500.311
1510.497
1520.0885
1530.655
1540.967
1550.172
1560.0905
1570.38
1580.949
1590.54
1600.332
1610.483
1620.779
1630.408
1640.0888
1650.166
1660.646
1670.445
1680.532
1690.029
170.0453
180.973
190.166
20.799
200.48
210.777
220.35
230.836
240.675
250.378
260.00774
270.731
280.407
290.0602
30.154
300.628
310.843
320.112
330.168
340.986
350.507
360.362
370.0454
380.585
390.235
40.381
400.168
410.358
420.599
430.29
440.103
450.599
460.232
470.288
480.186
490.269
50.41
500.594
510.715
520.167
530.459
540.643
550.777
560.5
570.819
580.373
590.275
60.456
600.0385
610.23
620.189
630.174
640.598
650.224
660.981
670.424
680.0106
690.881
70.0515
700.00535
710.0683
720.438
730.057
740.966
750.0211
760.668
770.143
780.0208
790.302
80.0905
800.925
810.873
820.0611
830.0562
840.128
850.0446
860.0777
870.0233
880.394
890.169
90.898
900.00794
910.514
920.293
930.377
940.712
950.0481
960.765
970.996
980.448
990.2



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: CNhs13199


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
0000060 (anatomical wall)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000160 (intestine)
0000331 (ileal mucosa)
0000344 (mucosa)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001168 (wall of small intestine)
0001204 (mucosa of small intestine)
0001242 (intestinal mucosa)
0001262 (wall of intestine)
0001555 (digestive tract)
0002050 (embryonic structure)
0002108 (small intestine)
0002116 (ileum)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004786 (gastrointestinal system mucosa)
0004921 (subdivision of digestive tract)
0004923 (organ component layer)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007026 (primitive gut)

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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