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FF:11301-117B5: 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 17:02, 29 March 2012


Name:Sebocyte, donor2
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-penis0.142
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-0.0961
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: CNhs11951

Jaspar motifP-value
MA0002.20.468
MA0003.10.38
MA0004.10.744
MA0006.10.147
MA0007.10.565
MA0009.10.154
MA0014.10.807
MA0017.10.249
MA0018.20.03
MA0019.10.943
MA0024.10.0115
MA0025.10.411
MA0027.10.3
MA0028.10.381
MA0029.10.285
MA0030.10.107
MA0031.10.00914
MA0035.20.449
MA0038.10.044
MA0039.20.367
MA0040.10.473
MA0041.10.67
MA0042.10.604
MA0043.10.0932
MA0046.10.148
MA0047.20.41
MA0048.10.78
MA0050.19.26128e-8
MA0051.11.69627e-5
MA0052.10.099
MA0055.10.341
MA0057.10.0175
MA0058.10.451
MA0059.10.212
MA0060.10.0432
MA0061.10.578
MA0062.20.0149
MA0065.20.0033
MA0066.10.098
MA0067.10.0123
MA0068.10.036
MA0069.10.103
MA0070.10.846
MA0071.10.813
MA0072.10.85
MA0073.10.736
MA0074.10.522
MA0076.10.0518
MA0077.10.742
MA0078.10.872
MA0079.20.875
MA0080.23.69426e-6
MA0081.10.0462
MA0083.10.718
MA0084.10.604
MA0087.10.562
MA0088.10.282
MA0090.10.0368
MA0091.10.354
MA0092.10.389
MA0093.10.595
MA0099.24.71045e-4
MA0100.10.102
MA0101.10.78
MA0102.20.0842
MA0103.13.85999e-5
MA0104.20.993
MA0105.10.101
MA0106.12.7018e-8
MA0107.10.723
MA0108.20.0742
MA0111.10.601
MA0112.20.00181
MA0113.10.436
MA0114.10.127
MA0115.10.548
MA0116.10.0157
MA0117.10.521
MA0119.10.113
MA0122.10.251
MA0124.10.161
MA0125.10.319
MA0131.10.201
MA0135.10.0789
MA0136.14.22083e-4
MA0137.20.00566
MA0138.20.0318
MA0139.10.403
MA0140.10.711
MA0141.10.359
MA0142.10.037
MA0143.10.68
MA0144.10.787
MA0145.10.0294
MA0146.10.267
MA0147.10.739
MA0148.10.535
MA0149.10.0271
MA0150.10.969
MA0152.10.843
MA0153.10.365
MA0154.10.0464
MA0155.10.301
MA0156.10.00251
MA0157.10.154
MA0159.10.291
MA0160.10.539
MA0162.10.0414
MA0163.10.00568
MA0164.10.144
MA0258.10.0542
MA0259.10.718



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: CNhs11951

Novel motifP-value
10.346
100.664
1000.628
1010.0646
1020.609
1030.0598
1040.667
1050.13
1060.00875
1070.0205
1080.121
1090.029
110.151
1100.161
1110.301
1120.0927
1130.277
1140.201
1150.233
1160.219
1170.38
1180.963
1190.173
120.841
1200.111
1210.684
1220.312
1230.635
1240.71
1250.877
1260.387
1270.251
1280.103
1290.174
130.149
1300.794
1310.748
1320.775
1330.0207
1340.738
1350.767
1360.294
1370.173
1380.877
1390.864
140.781
1400.431
1410.322
1420.0579
1430.267
1440.674
1450.0365
1460.0223
1470.161
1480.686
1490.188
150.395
1500.223
1510.246
1520.0155
1530.527
1540.866
1550.75
1560.897
1570.631
1580.145
1590.439
160.0245
1600.0287
1610.102
1620.325
1630.762
1640.441
1650.752
1660.624
1670.463
1680.234
1690.0152
170.0467
180.0773
190.319
20.176
200.678
210.426
220.37
230.319
240.0309
250.899
260.107
270.383
280.915
290.531
30.271
300.241
310.602
320.038
330.12
340.876
350.911
360.84
370.134
380.353
390.109
40.308
400.0284
410.632
420.582
430.287
440.26
450.252
460.2
470.127
480.0994
490.459
50.869
500.54
510.286
520.181
530.714
540.514
550.228
560.442
570.19
580.679
590.0545
60.372
600.216
610.921
620.513
630.103
640.269
650.261
660.784
670.564
680.817
690.316
70.408
700.0219
710.103
720.5
730.0286
740.0435
750.256
760.964
770.024
780.0776
790.0435
80.054
800.411
810.57
820.148
830.614
840.446
850.142
860.876
870.0318
880.233
890.0189
90.73
900.913
910.128
920.172
930.871
940.5
950.186
960.869
970.928
980.299
990.0336



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: CNhs11951


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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