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FF:11302-117B6: 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 16:59, 29 March 2012


Name:Gingival epithelial cells, donor2 (GEA14)
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 stage38 years old adult
sexfemale
age38
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-0.0456
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-lymphoma0.126
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: CNhs11896

Jaspar motifP-value
MA0002.20.773
MA0003.10.744
MA0004.10.107
MA0006.10.0147
MA0007.10.97
MA0009.10.184
MA0014.10.093
MA0017.10.914
MA0018.20.00755
MA0019.10.307
MA0024.10.0555
MA0025.10.863
MA0027.10.475
MA0028.10.237
MA0029.10.381
MA0030.10.369
MA0031.10.321
MA0035.20.261
MA0038.10.89
MA0039.29.65792e-4
MA0040.10.273
MA0041.10.34
MA0042.10.612
MA0043.10.151
MA0046.10.513
MA0047.20.63
MA0048.10.817
MA0050.10.145
MA0051.10.545
MA0052.10.0261
MA0055.10.00168
MA0057.10.0853
MA0058.10.0181
MA0059.10.694
MA0060.10.43
MA0061.10.647
MA0062.20.452
MA0065.20.631
MA0066.10.242
MA0067.10.0256
MA0068.10.0563
MA0069.10.467
MA0070.10.432
MA0071.10.0228
MA0072.10.311
MA0073.10.913
MA0074.10.307
MA0076.10.837
MA0077.10.178
MA0078.10.769
MA0079.20.25
MA0080.20.022
MA0081.10.21
MA0083.10.294
MA0084.10.183
MA0087.10.863
MA0088.10.836
MA0090.11.13285e-6
MA0091.10.348
MA0092.10.599
MA0093.10.0731
MA0099.24.16096e-16
MA0100.10.171
MA0101.10.116
MA0102.20.537
MA0103.15.73818e-7
MA0104.20.117
MA0105.10.988
MA0106.12.48529e-14
MA0107.10.0426
MA0108.20.678
MA0111.10.876
MA0112.20.522
MA0113.10.874
MA0114.10.808
MA0115.10.662
MA0116.10.625
MA0117.10.851
MA0119.10.196
MA0122.10.724
MA0124.10.507
MA0125.10.0404
MA0131.10.904
MA0135.10.456
MA0136.10.996
MA0137.20.552
MA0138.20.627
MA0139.10.971
MA0140.10.81
MA0141.10.0616
MA0142.10.257
MA0143.10.355
MA0144.10.72
MA0145.10.0535
MA0146.10.369
MA0147.10.268
MA0148.10.438
MA0149.10.0218
MA0150.10.122
MA0152.10.86
MA0153.10.815
MA0154.10.441
MA0155.10.485
MA0156.10.672
MA0157.10.422
MA0159.10.953
MA0160.10.651
MA0162.10.113
MA0163.10.632
MA0164.10.961
MA0258.10.581
MA0259.10.206



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: CNhs11896

Novel motifP-value
10.963
100.332
1000.555
1010.189
1020.45
1030.13
1040.866
1050.136
1060.151
1070.0663
1080.824
1090.0131
110.249
1100.484
1110.361
1120.156
1130.25
1140.346
1150.534
1160.745
1170.288
1180.871
1190.361
120.891
1200.102
1210.292
1220.54
1230.792
1240.0655
1250.249
1260.348
1270.224
1280.941
1290.103
130.0415
1300.718
1310.489
1320.34
1330.0071
1340.279
1350.636
1360.0307
1370.117
1380.923
1390.367
140.838
1400.678
1410.806
1420.708
1430.471
1440.224
1450.12
1460.0138
1470.114
1480.855
1490.825
150.881
1500.0709
1510.573
1520.00639
1530.971
1540.982
1550.827
1560.991
1570.136
1580.117
1590.476
160.0639
1600.625
1610.656
1620.309
1630.494
1640.898
1650.489
1660.37
1670.0877
1680.2
1690.11
170.342
180.414
190.701
20.442
200.575
210.678
220.591
230.15
240.0259
250.944
260.732
270.698
280.522
290.871
30.38
300.143
310.912
320.327
330.147
340.587
350.0725
360.563
370.147
380.506
390.167
40.932
400.0763
410.742
420.432
430.615
440.923
450.0209
460.721
470.317
480.121
490.479
50.904
500.42
510.826
520.0833
530.526
540.655
550.0913
560.393
570.56
580.801
590.48
60.458
600.177
610.686
620.856
630.168
640.747
650.934
660.227
670.735
680.145
690.759
70.372
700.165
710.56
720.954
730.00228
740.077
750.323
760.998
770.0327
780.0149
790.365
80.804
800.515
810.196
820.571
830.608
840.974
850.557
860.77
877.29673e-4
880.816
890.154
90.832
900.43
910.764
920.715
930.52
940.46
950.27
960.86
970.31
980.718
990.0955



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: CNhs11896


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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