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FF:11220-116B5: 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 16:34, 29 March 2012


Name:Sebocyte, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stage29 years old adult
sexmale
ageNA
cell typesebocyte
cell lineNA
companyN/A
collaborationWeonju Lee (Kyungpook National University School of Medicine)
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-0.0991
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: CNhs10847

Jaspar motifP-value
MA0002.20.471
MA0003.10.554
MA0004.10.861
MA0006.10.0791
MA0007.10.557
MA0009.10.0649
MA0014.10.822
MA0017.10.309
MA0018.20.213
MA0019.10.61
MA0024.17.99244e-4
MA0025.10.852
MA0027.10.399
MA0028.10.713
MA0029.10.166
MA0030.10.937
MA0031.10.648
MA0035.20.672
MA0038.10.731
MA0039.20.0153
MA0040.10.578
MA0041.10.388
MA0042.10.871
MA0043.10.87
MA0046.10.297
MA0047.20.487
MA0048.10.919
MA0050.10.00857
MA0051.10.048
MA0052.10.514
MA0055.10.0254
MA0057.10.131
MA0058.10.723
MA0059.10.382
MA0060.10.778
MA0061.10.4
MA0062.20.164
MA0065.20.0322
MA0066.10.619
MA0067.10.00718
MA0068.10.361
MA0069.10.271
MA0070.10.375
MA0071.10.399
MA0072.10.69
MA0073.10.702
MA0074.10.669
MA0076.10.15
MA0077.10.472
MA0078.10.848
MA0079.20.233
MA0080.20.0646
MA0081.10.23
MA0083.10.376
MA0084.10.126
MA0087.10.792
MA0088.10.567
MA0090.10.00146
MA0091.10.847
MA0092.10.442
MA0093.10.804
MA0099.21.05774e-17
MA0100.10.298
MA0101.10.111
MA0102.20.165
MA0103.12.08682e-4
MA0104.20.73
MA0105.10.881
MA0106.11.03622e-9
MA0107.10.0843
MA0108.21.50248e-6
MA0111.10.755
MA0112.20.137
MA0113.10.362
MA0114.10.179
MA0115.10.812
MA0116.10.482
MA0117.10.374
MA0119.10.195
MA0122.10.922
MA0124.10.461
MA0125.10.0276
MA0131.10.205
MA0135.10.0953
MA0136.10.784
MA0137.20.373
MA0138.20.595
MA0139.10.919
MA0140.10.61
MA0141.10.857
MA0142.10.0856
MA0143.10.656
MA0144.10.638
MA0145.10.0459
MA0146.10.45
MA0147.10.915
MA0148.10.197
MA0149.10.159
MA0150.10.271
MA0152.10.832
MA0153.10.593
MA0154.10.0916
MA0155.10.393
MA0156.10.903
MA0157.10.428
MA0159.10.856
MA0160.10.714
MA0162.10.0512
MA0163.10.85
MA0164.10.262
MA0258.10.582
MA0259.10.284



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: CNhs10847

Novel motifP-value
10.719
100.0756
1000.846
1010.0561
1020.623
1030.306
1040.506
1050.0049
1060.0527
1070.0197
1080.814
1090.0445
110.426
1100.306
1110.885
1120.511
1130.64
1140.802
1150.235
1160.696
1170.98
1180.647
1190.5
120.476
1200.36
1210.165
1220.0971
1230.0985
1240.231
1250.581
1260.923
1270.4
1280.458
1290.151
130.068
1300.0971
1310.694
1320.458
1330.0108
1340.93
1350.993
1360.704
1370.237
1380.834
1390.288
140.659
1400.831
1410.571
1420.187
1430.479
1440.14
1450.151
1460.00969
1470.316
1480.118
1490.473
150.985
1500.204
1510.355
1520.00868
1530.54
1540.535
1550.377
1560.572
1570.685
1580.274
1590.622
160.1
1600.179
1610.774
1620.791
1630.937
1640.731
1650.55
1660.578
1670.0665
1680.226
1690.054
170.0568
180.164
190.661
20.0915
200.894
210.471
220.348
230.316
240.0129
250.725
260.551
270.586
280.814
290.813
30.894
300.0481
310.746
320.905
330.26
340.402
350.362
360.411
370.44
380.359
390.0967
40.628
400.00484
410.671
420.79
430.521
440.213
450.0618
460.787
470.539
480.314
490.797
50.955
500.226
510.538
520.0611
530.941
540.606
550.851
560.209
570.383
580.814
590.169
60.078
600.112
610.786
620.608
630.114
640.509
650.568
660.297
670.412
680.632
690.959
70.307
700.31
710.358
720.88
730.015
740.0767
750.991
760.821
770.0056
780.331
790.854
80.41
800.232
810.261
820.772
830.731
840.689
850.879
860.452
870.0877
880.652
890.109
90.484
900.709
910.373
920.373
930.303
940.823
950.131
960.714
970.145
980.547
990.053



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: CNhs10847


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)
0000150 (glandular epithelial cell)
0000151 (secretory cell)
0000154 (protein secreting cell)
0000255 (eukaryotic cell)
0000317 (sebum secreting cell)
0000548 (animal cell)
0000622 (acinar cell)
0002140 (acinar cell of sebaceous gland)
0002371 (somatic cell)
1000448 (epithelial cell of sweat gland)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001003 (skin epidermis)
0001062 (anatomical entity)
0001820 (sweat gland)
0001821 (sebaceous gland)
0002050 (embryonic structure)
0002097 (skin of body)
0002199 (integument)
0002330 (exocrine system)
0002365 (exocrine gland)
0002416 (integumental system)
0002419 (skin gland)
0002530 (gland)
0002532 (epiblast (generic))
0003102 (surface structure)
0003297 (gland of integumental system)
0003487 (skin sebaceous gland)
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)
0007376 (outer epithelium)
0007383 (enveloping layer of ectoderm)
0007771 (epidermis gland)

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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