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FF:12142-128E9: 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 17:21, 29 March 2012


Name:Mallassez-derived cells, donor1 (MZH3)
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 stageNA
sexmale
age22 years old adult
cell typeepithelial cell rests of Malassez
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-0.168
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-0.143
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: CNhs12538

Jaspar motifP-value
MA0002.20.104
MA0003.10.284
MA0004.10.707
MA0006.10.263
MA0007.10.543
MA0009.10.0314
MA0014.10.0515
MA0017.10.0571
MA0018.20.0311
MA0019.10.706
MA0024.10.00483
MA0025.10.711
MA0027.10.476
MA0028.10.0934
MA0029.10.136
MA0030.10.924
MA0031.10.647
MA0035.20.677
MA0038.10.508
MA0039.20.0018
MA0040.10.719
MA0041.10.312
MA0042.10.903
MA0043.10.154
MA0046.10.46
MA0047.20.185
MA0048.10.549
MA0050.10.00308
MA0051.10.154
MA0052.10.665
MA0055.10.121
MA0057.10.0843
MA0058.10.718
MA0059.10.169
MA0060.10.0346
MA0061.10.426
MA0062.20.0722
MA0065.20.0438
MA0066.10.076
MA0067.10.129
MA0068.10.00273
MA0069.10.934
MA0070.10.803
MA0071.10.733
MA0072.10.864
MA0073.10.967
MA0074.10.305
MA0076.10.19
MA0077.10.648
MA0078.10.413
MA0079.20.883
MA0080.20.586
MA0081.10.931
MA0083.10.989
MA0084.10.26
MA0087.10.838
MA0088.10.0505
MA0090.17.69454e-4
MA0091.10.817
MA0092.10.206
MA0093.10.74
MA0099.24.05256e-19
MA0100.10.097
MA0101.10.243
MA0102.20.25
MA0103.17.73464e-5
MA0104.20.812
MA0105.10.22
MA0106.12.10042e-10
MA0107.10.208
MA0108.20.0134
MA0111.10.629
MA0112.20.0244
MA0113.10.544
MA0114.10.052
MA0115.10.752
MA0116.10.147
MA0117.10.86
MA0119.10.114
MA0122.10.605
MA0124.10.238
MA0125.10.104
MA0131.10.878
MA0135.10.759
MA0136.10.0179
MA0137.20.722
MA0138.20.443
MA0139.10.416
MA0140.10.125
MA0141.10.779
MA0142.10.0869
MA0143.10.431
MA0144.10.375
MA0145.10.0527
MA0146.10.436
MA0147.10.638
MA0148.10.092
MA0149.10.0208
MA0150.10.00137
MA0152.10.38
MA0153.10.791
MA0154.10.0825
MA0155.10.801
MA0156.10.0362
MA0157.10.634
MA0159.10.49
MA0160.10.511
MA0162.10.0329
MA0163.10.15
MA0164.10.734
MA0258.10.714
MA0259.10.733



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: CNhs12538

Novel motifP-value
10.328
100.969
1000.743
1010.609
1020.732
1030.157
1040.765
1050.0706
1060.253
1070.312
1080.819
1090.00455
110.121
1100.186
1110.458
1120.145
1130.695
1140.192
1150.065
1160.993
1170.379
1180.593
1190.36
120.888
1200.115
1210.885
1220.136
1230.205
1240.511
1250.415
1260.258
1270.0362
1280.861
1290.0611
130.0265
1300.527
1310.279
1320.836
1330.0166
1340.97
1350.549
1360.292
1370.624
1380.48
1390.702
140.682
1400.355
1410.722
1420.477
1430.0764
1440.751
1450.288
1460.0116
1470.488
1480.228
1490.843
150.206
1500.552
1510.304
1520.0267
1530.16
1540.686
1550.381
1560.817
1570.751
1580.769
1590.4
160.145
1600.341
1610.5
1620.579
1630.938
1640.953
1650.496
1660.995
1670.683
1680.215
1690.0548
170.181
180.124
190.862
20.227
200.956
210.872
220.427
230.159
240.0189
250.363
260.819
270.194
280.425
290.388
30.26
300.194
310.583
320.509
330.127
340.825
350.386
360.323
370.0575
380.312
390.548
40.564
400.0106
410.933
420.277
430.308
440.566
450.0515
460.439
470.0992
480.129
490.592
50.499
500.603
510.812
520.332
530.768
540.355
550.285
560.312
570.215
580.377
590.318
60.632
600.13
610.726
620.371
630.181
640.271
650.423
660.166
670.58
680.0433
690.891
70.077
700.0177
710.17
720.323
730.00591
740.532
750.2
760.709
770.0262
780.0328
790.109
80.207
800.465
810.938
820.613
830.173
840.413
850.173
860.955
870.0264
880.723
890.00702
90.664
900.647
910.89
920.502
930.064
940.42
950.00257
960.4
970.457
980.251
990.151



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: CNhs12538


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)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002077 (ecto-epithelial cell)
0002159 (general ecto-epithelial cell)
0002166 (epithelial cell of Malassez)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000075 (subdivision of skeletal system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001708 (jaw skeleton)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002342 (neural crest)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002539 (pharyngeal arch)
0003059 (presomitic mesoderm)
0003075 (neural plate)
0003077 (paraxial mesoderm)
0003089 (sclerotome)
0003104 (mesenchyme)
0003129 (skull)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004288 (skeleton)
0004765 (skeletal element)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007284 (presumptive neural plate)
0008814 (pharyngeal arch system)
0008816 (embryonic head)
0009142 (entire embryonic mesenchyme)

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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