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|rna_weight_ug=0.5225
|rna_weight_ug=0.5225
|sample_age=
|sample_age=
|sample_category=tissues
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_line=

Revision as of 16:15, 26 December 2012


Name:Ileum epithelium, pool2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:tissues
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_b
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]


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

CNhs13232

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10050.177
1006-0.351
1007-0.117
10081.964
1009-0.19
101-0.172
10100
1011-0.298
10120
10130.266
1014-0.0874
1015-0.424
1016-0.594
10170
10180.245
10190
1020
10200
10210
1022-0.0264
10230
1024-0.307
10250
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-0.911
10320.751
1033-0.00394
10340.156
10350
1036-0.111
10370
10380.0793
10390.198
1040
1040-0.546
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



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: CNhs13232

Jaspar motifP-value
MA0002.20.00226
MA0003.10.294
MA0004.10.532
MA0006.10.0824
MA0007.10.188
MA0009.10.371
MA0014.10.0526
MA0017.13.8895e-28
MA0018.20.279
MA0019.10.176
MA0024.10.175
MA0025.10.355
MA0027.10.348
MA0028.10.00404
MA0029.10.467
MA0030.10.739
MA0031.10.468
MA0035.24.63856e-5
MA0038.10.881
MA0039.28.36757e-5
MA0040.10.006
MA0041.10.333
MA0042.10.436
MA0043.10.108
MA0046.18.96583e-53
MA0047.20.0066
MA0048.10.3
MA0050.17.09907e-7
MA0051.13.73292e-7
MA0052.19.54187e-4
MA0055.10.299
MA0057.10.136
MA0058.10.61
MA0059.10.651
MA0060.10.484
MA0061.10.457
MA0062.21.38613e-6
MA0065.25.02225e-14
MA0066.10.112
MA0067.10.451
MA0068.10.214
MA0069.10.635
MA0070.10.0893
MA0071.10.114
MA0072.10.892
MA0073.10.805
MA0074.10.224
MA0076.10.0122
MA0077.10.869
MA0078.10.755
MA0079.20.74
MA0080.21.51114e-6
MA0081.10.822
MA0083.10.00288
MA0084.10.26
MA0087.10.408
MA0088.10.181
MA0090.10.87
MA0091.10.744
MA0092.10.891
MA0093.10.613
MA0099.21.37367e-5
MA0100.10.717
MA0101.10.395
MA0102.20.468
MA0103.14.3532e-7
MA0104.20.549
MA0105.10.543
MA0106.10.485
MA0107.10.471
MA0108.20.373
MA0111.10.892
MA0112.26.73084e-4
MA0113.10.208
MA0114.12.75598e-31
MA0115.15.45715e-13
MA0116.10.289
MA0117.10.654
MA0119.10.0909
MA0122.10.757
MA0124.10.181
MA0125.10.74
MA0131.10.693
MA0135.10.405
MA0136.19.74748e-12
MA0137.20.0373
MA0138.20.996
MA0139.10.0804
MA0140.10.0131
MA0141.14.6358e-7
MA0142.10.232
MA0143.10.0975
MA0144.10.0112
MA0145.10.0161
MA0146.10.131
MA0147.10.67
MA0148.10.00685
MA0149.10.00656
MA0150.10.0557
MA0152.10.0799
MA0153.11.2829e-41
MA0154.10.119
MA0155.10.517
MA0156.11.25198e-7
MA0157.10.95
MA0159.12.2059e-4
MA0160.11.10584e-4
MA0162.10.65
MA0163.10.141
MA0164.10.792
MA0258.10.0376
MA0259.10.828



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: CNhs13232

Novel motifP-value
10.126
100.105
1000.733
1010.76
1020.568
1030.227
1040.894
1050.216
1060.0465
1070.246
1080.943
1090.0357
110.109
1100.224
1110.294
1120.0218
1130.456
1140.0593
1150.832
1160.223
1170.0247
1180.381
1190.259
120.674
1200.531
1210.584
1220.824
1230.0431
1240.1
1250.169
1260.0412
1270.212
1280.355
1290.254
139.35114e-5
1300.642
1310.627
1320.524
1330.81
1340.999
1350.154
1360.0219
1370.756
1380.0852
1390.0866
140.727
1400.208
1410.222
1421
1430.236
1440.318
1450.0907
1460.292
1470.96
1480.624
1490.989
150.0901
1500.372
1510.637
1520.0737
1530.848
1540.833
1550.291
1560.0586
1570.461
1580.624
1590.655
1600.716
1610.657
1620.911
1630.299
1640.0792
1650.295
1660.748
1670.618
1680.883
1690.0428
170.0413
180.909
190.247
20.725
200.437
210.878
220.33
230.957
240.546
250.344
260.00915
270.736
280.334
290.0839
30.174
300.454
310.958
320.2
330.164
340.933
350.635
360.406
370.0389
380.52
390.289
40.476
400.137
410.249
420.645
430.359
440.138
450.488
460.272
470.335
480.184
490.278
50.444
500.62
510.744
520.184
530.445
540.598
550.619
560.606
570.958
580.279
590.265
60.544
600.0474
610.22
620.229
630.189
640.557
650.326
660.829
670.291
680.195
690.851
70.0525
700.0173
710.0995
720.245
730.0371
740.682
750.0296
760.648
770.192
780.0144
790.69
80.148
800.603
810.884
820.132
830.0467
840.125
850.131
860.0649
870.00766
880.28
890.181
90.914
900.111
910.613
920.469
930.516
940.451
950.00528
960.877
970.932
980.517
990.264



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: CNhs13232


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0002108 (small intestine)
0000160 (intestine)
0000331 (ileal mucosa)
0000483 (epithelium)
0002116 (ileum)
0001242 (intestinal mucosa)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0001204 (mucosa of small intestine)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001168 (wall of small intestine)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011274 (mouse Ileum epithelium sample)

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
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)

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