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|name=CD326+ enterocyte, pool2
|name=CD326+ enterocyte, pool2
|sample_id=11849
|sample_id=11849
|rna_tube_id=
|rna_tube_id=124I4
|rna_box=124
|rna_box=124
|rna_position=I4
|rna_position=I4
Line 20: Line 20:
|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=1.78000
|rna_od260/230=1.78
|rna_od260/280=2.17000
|rna_od260/280=2.17
|sample_cell_type=enterocyte
|sample_cell_type=enterocyte
|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=1.12750
|rna_weight_ug=1.1275
|rna_concentration=0.10250
|rna_concentration=0.1025
|sample_note=
|sample_note=
|profile_hcage=CNhs13197,LSID1004,release012,MAPPING
|profile_hcage=CNhs13197,LSID1004,release012,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:12, 27 February 2012


Name:CD326+ enterocyte, pool2
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 stageadult
sexmale
ageNA
cell typeenterocyte
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberCont_Ep+_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]





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

CNhs13197

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10050.0745
1006-0.317
10070.0722
10081.448
1009-0.19
101-0.51
10100
1011-0.337
10120
10130.222
1014-0.0874
1015-0.584
1016-0.488
10170
10180.478
10190
1020
10200
10210.603
1022-0.0704
10230
1024-0.307
10250
10260
1027-0.048
10280
1029-0.115
103-0.0887
10300
1031-1.148
10320.896
10330.12
10340
10350
10360.196
10370
10380.415
1039-0.0514
1040
1040-0.884
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: CNhs13197

Jaspar motifP-value
MA0002.20.0202
MA0003.10.642
MA0004.10.61
MA0006.10.036
MA0007.10.217
MA0009.10.12
MA0014.10.0535
MA0017.18.60242e-40
MA0018.20.00727
MA0019.10.0886
MA0024.11.46652e-4
MA0025.10.299
MA0027.10.279
MA0028.10.237
MA0029.10.85
MA0030.10.275
MA0031.10.0465
MA0035.29.7584e-7
MA0038.10.513
MA0039.21.03939e-4
MA0040.10.0917
MA0041.10.158
MA0042.10.219
MA0043.10.338
MA0046.16.84917e-49
MA0047.20.0409
MA0048.10.137
MA0050.18.26523e-5
MA0051.13.82717e-7
MA0052.10.744
MA0055.10.167
MA0057.10.122
MA0058.10.602
MA0059.10.489
MA0060.10.297
MA0061.10.766
MA0062.20.0137
MA0065.21.09392e-17
MA0066.10.193
MA0067.10.198
MA0068.10.125
MA0069.10.758
MA0070.10.611
MA0071.10.00813
MA0072.10.419
MA0073.10.813
MA0074.10.233
MA0076.10.33
MA0077.10.431
MA0078.10.799
MA0079.20.169
MA0080.20.0643
MA0081.10.451
MA0083.10.549
MA0084.10.286
MA0087.10.357
MA0088.10.501
MA0090.10.908
MA0091.10.0846
MA0092.10.914
MA0093.10.654
MA0099.21.02887e-6
MA0100.10.615
MA0101.10.595
MA0102.20.917
MA0103.18.42809e-7
MA0104.20.0541
MA0105.10.0958
MA0106.10.925
MA0107.10.678
MA0108.20.0425
MA0111.10.616
MA0112.20.0289
MA0113.10.537
MA0114.13.00312e-53
MA0115.15.07003e-17
MA0116.10.0911
MA0117.10.0995
MA0119.10.0613
MA0122.10.564
MA0124.10.591
MA0125.10.691
MA0131.10.845
MA0135.10.103
MA0136.10.00151
MA0137.20.78
MA0138.20.658
MA0139.10.619
MA0140.10.0219
MA0141.11.42074e-10
MA0142.10.0445
MA0143.10.0647
MA0144.10.0583
MA0145.10.0134
MA0146.10.066
MA0147.10.0404
MA0148.10.0203
MA0149.10.0128
MA0150.10.0334
MA0152.10.0712
MA0153.16.62693e-40
MA0154.10.606
MA0155.10.418
MA0156.10.014
MA0157.10.474
MA0159.18.02461e-4
MA0160.11.403e-7
MA0162.10.487
MA0163.10.417
MA0164.10.613
MA0258.10.0821
MA0259.10.662



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: CNhs13197

Novel motifP-value
10.284
100.498
1000.569
1010.804
1020.69
1030.807
1040.823
1050.338
1060.0492
1070.413
1080.5
1090.308
110.258
1100.565
1110.134
1120.0482
1130.187
1140.0731
1150.575
1160.328
1170.07
1180.61
1190.263
120.654
1200.943
1210.43
1220.813
1230.0378
1240.113
1250.427
1260.103
1270.628
1280.0834
1290.585
131.11912e-5
1300.605
1310.996
1320.411
1330.228
1340.608
1350.0661
1360.00479
1370.273
1380.191
1390.359
140.773
1400.575
1410.834
1420.369
1430.169
1440.301
1450.228
1460.434
1470.812
1480.663
1490.394
150.259
1500.28
1510.789
1520.0641
1530.574
1540.671
1550.323
1560.145
1570.477
1580.332
1590.572
1600.325
1610.831
1620.851
1630.12
1640.256
1650.948
1660.443
1670.837
1680.739
1690.198
170.0807
180.716
190.693
20.969
200.191
210.948
220.28
230.268
240.95
250.376
260.0377
270.545
280.31
290.448
30.333
300.325
310.949
320.499
330.207
340.807
350.77
360.851
370.0184
380.692
390.434
40.497
400.3
410.226
420.737
430.749
440.441
450.357
460.636
470.925
480.555
490.479
50.99
500.808
510.832
520.134
530.285
540.456
550.358
560.801
570.486
580.402
590.544
60.908
600.0348
610.704
620.301
630.365
640.914
650.459
660.586
670.183
680.0345
690.827
70.0496
700.0197
710.328
720.643
730.0134
740.727
750.0674
760.753
770.168
780.014
790.794
80.996
800.867
810.804
820.2
830.657
840.0264
850.193
860.0785
870.00975
880.303
890.738
90.665
900.822
910.719
920.939
930.174
940.279
950.0702
960.679
970.901
980.964
990.897



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: CNhs13197


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000075 (columnar/cuboidal epithelial cell)
0000212 (absorptive cell)
0000223 (endodermal cell)
0000239 (brush border epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000584 (enterocyte)
0000677 (gut absorptive cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0002321 (embryonic cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)

UBERON: Anatomy
0000060 (anatomical wall)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000160 (intestine)
0000344 (mucosa)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000485 (simple columnar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001242 (intestinal mucosa)
0001262 (wall of intestine)
0001277 (intestinal epithelium)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003350 (epithelium of mucosa)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004786 (gastrointestinal system mucosa)
0004808 (gastrointestinal system epithelium)
0004921 (subdivision of digestive tract)
0004923 (organ component layer)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
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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