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FF:11221-116B6: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 16:38, 29 March 2012


Name:Gingival epithelial cells, donor1 (GEA11)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuegum
dev stage61 years old adult
sexfemale
age61
cell typeepithelial cell
cell lineNA
companyN/A
collaborationMitsuhiro Ohshima (Nihon University School of Dentistry)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.1
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.0845
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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: CNhs11061

Jaspar motifP-value
MA0002.20.936
MA0003.10.508
MA0004.10.367
MA0006.10.0147
MA0007.10.991
MA0009.10.0886
MA0014.10.102
MA0017.10.764
MA0018.21.00125e-4
MA0019.10.363
MA0024.10.00116
MA0025.10.122
MA0027.10.253
MA0028.10.483
MA0029.10.369
MA0030.10.765
MA0031.10.762
MA0035.20.423
MA0038.10.197
MA0039.20.00117
MA0040.10.417
MA0041.10.346
MA0042.10.901
MA0043.10.00376
MA0046.10.742
MA0047.20.369
MA0048.10.673
MA0050.10.0116
MA0051.10.212
MA0052.10.0592
MA0055.10.0359
MA0057.10.153
MA0058.10.215
MA0059.10.589
MA0060.10.0148
MA0061.10.944
MA0062.20.852
MA0065.20.646
MA0066.10.0676
MA0067.10.0396
MA0068.10.239
MA0069.10.844
MA0070.10.745
MA0071.10.184
MA0072.10.854
MA0073.10.864
MA0074.10.54
MA0076.10.824
MA0077.10.193
MA0078.10.722
MA0079.20.174
MA0080.20.043
MA0081.10.257
MA0083.10.359
MA0084.10.0781
MA0087.10.84
MA0088.10.905
MA0090.18.98103e-6
MA0091.10.0568
MA0092.10.524
MA0093.10.345
MA0099.23.04024e-21
MA0100.10.073
MA0101.10.66
MA0102.20.376
MA0103.16.56969e-7
MA0104.20.137
MA0105.10.63
MA0106.13.02377e-11
MA0107.10.518
MA0108.20.668
MA0111.10.747
MA0112.20.225
MA0113.10.818
MA0114.10.562
MA0115.10.548
MA0116.10.842
MA0117.10.512
MA0119.10.816
MA0122.10.863
MA0124.10.434
MA0125.10.0491
MA0131.10.656
MA0135.10.648
MA0136.10.988
MA0137.20.445
MA0138.20.67
MA0139.10.629
MA0140.10.627
MA0141.10.266
MA0142.10.778
MA0143.10.68
MA0144.10.472
MA0145.10.0284
MA0146.10.168
MA0147.10.208
MA0148.10.24
MA0149.10.0659
MA0150.10.124
MA0152.10.254
MA0153.10.483
MA0154.10.41
MA0155.10.861
MA0156.10.941
MA0157.10.384
MA0159.10.6
MA0160.10.58
MA0162.10.131
MA0163.10.482
MA0164.10.836
MA0258.10.789
MA0259.10.15



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: CNhs11061

Novel motifP-value
10.674
100.49
1000.972
1010.0281
1020.356
1030.0775
1040.715
1050.254
1060.0452
1070.0869
1080.531
1090.00617
110.527
1100.541
1110.447
1120.236
1130.128
1140.378
1150.858
1160.635
1170.387
1180.892
1190.273
120.931
1200.0526
1210.392
1220.0595
1230.143
1240.0108
1250.898
1260.404
1270.462
1280.482
1290.128
130.169
1300.875
1310.251
1320.463
1330.0303
1340.481
1350.697
1360.00829
1370.351
1380.906
1390.673
140.703
1400.88
1410.965
1420.671
1430.667
1440.264
1450.0945
1460.0295
1470.199
1480.834
1490.993
150.829
1500.13
1510.473
1520.00515
1530.618
1540.779
1550.771
1560.969
1570.544
1580.101
1590.352
160.0682
1600.578
1610.82
1620.268
1630.254
1640.759
1650.0832
1660.334
1670.0593
1680.145
1690.132
170.376
180.556
190.658
20.223
200.777
210.583
220.302
230.296
240.00729
250.988
260.613
270.4
280.625
290.674
30.603
300.0623
310.803
320.162
330.12
340.958
350.0781
360.616
370.163
380.588
390.202
40.646
400.0524
410.998
420.746
430.685
440.442
450.0299
460.885
470.662
480.219
490.383
50.945
500.307
510.824
520.125
530.448
540.701
550.0913
560.289
570.752
580.98
590.309
60.422
600.139
610.65
620.528
630.137
640.898
650.781
660.638
670.557
680.0619
690.263
70.311
700.0611
710.857
720.529
730.00109
740.0434
750.436
760.811
770.00578
780.0281
790.53
80.729
800.924
810.388
820.597
830.831
840.971
850.382
860.79
870.0027
880.899
890.0541
90.924
900.567
910.986
920.932
930.998
940.211
950.109
960.542
970.346
980.862
990.0665



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: CNhs11061


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002371 (somatic cell)
0002621 (gingival epithelial cell)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000153 (anterior region of body)
0000161 (orifice)
0000165 (mouth)
0000166 (oral opening)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000930 (stomodeum)
0001004 (respiratory system)
0001007 (digestive system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0001828 (gingiva)
0001949 (gingival epithelium)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003929 (gut epithelium)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004807 (respiratory system epithelium)
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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