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FF:11379-118B2: 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 17:00, 29 March 2012


Name:Gingival epithelial cells, donor3 (GEA15)
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 stage47 years old adult
sexmale
age47
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-0.133
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-lymphoma0.071
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
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C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
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: CNhs11903

Jaspar motifP-value
MA0002.20.982
MA0003.10.672
MA0004.10.357
MA0006.10.0173
MA0007.10.939
MA0009.10.0199
MA0014.10.166
MA0017.10.605
MA0018.20.00131
MA0019.10.496
MA0024.10.0525
MA0025.10.975
MA0027.10.231
MA0028.10.0731
MA0029.10.192
MA0030.10.986
MA0031.10.748
MA0035.20.641
MA0038.10.758
MA0039.20.00233
MA0040.10.485
MA0041.10.262
MA0042.10.931
MA0043.10.289
MA0046.10.309
MA0047.20.417
MA0048.10.539
MA0050.10.137
MA0051.10.948
MA0052.10.0204
MA0055.10.0442
MA0057.10.146
MA0058.10.267
MA0059.10.934
MA0060.10.52
MA0061.10.861
MA0062.20.0685
MA0065.20.872
MA0066.10.496
MA0067.10.0316
MA0068.10.15
MA0069.10.829
MA0070.10.558
MA0071.10.0788
MA0072.10.572
MA0073.10.851
MA0074.10.524
MA0076.10.198
MA0077.10.383
MA0078.10.583
MA0079.20.0509
MA0080.20.0341
MA0081.10.792
MA0083.10.0782
MA0084.10.125
MA0087.10.545
MA0088.10.563
MA0090.14.13806e-6
MA0091.10.0814
MA0092.10.688
MA0093.10.348
MA0099.22.41438e-17
MA0100.10.171
MA0101.10.188
MA0102.20.984
MA0103.14.17327e-7
MA0104.20.286
MA0105.10.307
MA0106.14.10331e-12
MA0107.10.294
MA0108.20.169
MA0111.10.259
MA0112.20.751
MA0113.10.175
MA0114.10.566
MA0115.10.704
MA0116.10.317
MA0117.10.473
MA0119.10.911
MA0122.10.977
MA0124.10.536
MA0125.10.0361
MA0131.10.756
MA0135.10.611
MA0136.10.637
MA0137.20.912
MA0138.20.649
MA0139.10.834
MA0140.10.749
MA0141.10.0706
MA0142.10.334
MA0143.10.47
MA0144.10.33
MA0145.10.0117
MA0146.10.586
MA0147.10.402
MA0148.10.331
MA0149.10.105
MA0150.10.116
MA0152.10.252
MA0153.10.314
MA0154.10.92
MA0155.10.277
MA0156.10.292
MA0157.10.48
MA0159.10.431
MA0160.10.59
MA0162.10.215
MA0163.10.29
MA0164.10.887
MA0258.10.181
MA0259.10.249



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: CNhs11903

Novel motifP-value
10.408
100.162
1000.737
1010.0322
1020.225
1030.062
1040.82
1050.13
1060.275
1070.12
1080.499
1090.00947
110.899
1100.496
1110.715
1120.765
1130.119
1140.892
1150.785
1160.17
1170.333
1180.863
1190.781
120.957
1200.0949
1210.362
1220.0738
1230.24
1240.034
1250.431
1260.29
1270.274
1280.944
1290.0608
130.171
1300.572
1310.318
1320.528
1330.0148
1340.53
1350.697
1360.00797
1370.152
1380.676
1390.0587
140.672
1400.955
1410.592
1420.82
1430.304
1440.0687
1450.411
1460.00537
1470.154
1480.611
1490.359
150.722
1500.159
1510.652
1520.00369
1530.759
1540.936
1550.598
1560.633
1570.277
1580.0872
1590.372
160.129
1600.688
1610.89
1620.851
1630.307
1640.765
1650.375
1660.183
1670.0527
1680.286
1690.289
170.662
180.912
190.208
20.28
200.723
210.179
220.607
230.386
240.00702
250.939
260.672
270.766
280.368
290.711
30.935
300.0436
310.847
320.00932
330.162
340.866
350.022
360.516
370.514
380.708
390.194
40.966
400.12
410.538
420.868
430.764
440.539
450.0102
460.469
470.987
480.427
490.174
50.608
500.347
510.928
520.151
530.443
540.886
550.375
560.565
570.645
580.967
590.544
60.111
600.25
610.714
620.312
630.305
640.762
650.729
660.308
670.771
680.0173
690.919
70.486
700.466
710.321
720.952
738.30859e-4
740.0121
750.898
760.986
770.0782
780.0149
790.208
80.638
800.975
810.183
820.224
830.632
840.864
850.967
860.753
870.00133
880.622
890.241
90.856
900.964
910.848
920.629
930.972
940.279
950.208
960.59
970.324
980.713
990.0674



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: CNhs11903


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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