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FF:11935-125I9: 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 17:40, 29 March 2012


Name:Olfactory epithelial cells, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexmale
age61
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
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-penis0.0103
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-0.198
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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: CNhs13818

Jaspar motifP-value
MA0002.20.0155
MA0003.10.535
MA0004.10.134
MA0006.10.338
MA0007.10.902
MA0009.10.635
MA0014.10.427
MA0017.10.097
MA0018.21.13062e-6
MA0019.10.0797
MA0024.11.4876e-5
MA0025.15.88859e-4
MA0027.10.831
MA0028.10.0682
MA0029.10.585
MA0030.10.0084
MA0031.10.0504
MA0035.20.00291
MA0038.10.0256
MA0039.20.0127
MA0040.10.394
MA0041.10.235
MA0042.10.766
MA0043.13.36334e-5
MA0046.10.0567
MA0047.20.134
MA0048.10.00167
MA0050.10.933
MA0051.10.596
MA0052.10.0189
MA0055.10.451
MA0057.10.103
MA0058.10.00543
MA0059.10.729
MA0060.11.21497e-15
MA0061.10.088
MA0062.21.36147e-7
MA0065.20.802
MA0066.10.491
MA0067.10.00508
MA0068.10.989
MA0069.10.201
MA0070.10.551
MA0071.10.898
MA0072.10.161
MA0073.10.216
MA0074.10.354
MA0076.10.00232
MA0077.10.852
MA0078.10.986
MA0079.20.184
MA0080.28.947e-9
MA0081.10.00163
MA0083.10.0441
MA0084.10.1
MA0087.10.842
MA0088.10.658
MA0090.11.19193e-5
MA0091.10.0926
MA0092.10.0855
MA0093.10.0522
MA0099.27.04566e-6
MA0100.10.286
MA0101.10.00275
MA0102.20.596
MA0103.10.103
MA0104.20.0206
MA0105.10.529
MA0106.10.0417
MA0107.10.00621
MA0108.20.0279
MA0111.10.86
MA0112.20.00959
MA0113.10.398
MA0114.10.259
MA0115.10.0981
MA0116.10.329
MA0117.10.0328
MA0119.10.00349
MA0122.10.149
MA0124.10.612
MA0125.10.493
MA0131.10.61
MA0135.10.109
MA0136.17.34585e-12
MA0137.20.0688
MA0138.20.677
MA0139.10.733
MA0140.10.00243
MA0141.10.885
MA0142.10.286
MA0143.10.731
MA0144.10.872
MA0145.10.747
MA0146.10.454
MA0147.10.123
MA0148.10.186
MA0149.10.367
MA0150.10.00764
MA0152.10.0296
MA0153.10.146
MA0154.10.964
MA0155.10.523
MA0156.12.83992e-10
MA0157.10.0938
MA0159.10.643
MA0160.10.0289
MA0162.10.0113
MA0163.10.00974
MA0164.10.849
MA0258.10.243
MA0259.10.408



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: CNhs13818

Novel motifP-value
10.891
100.157
1000.54
1010.78
1020.0841
1030.779
1040.867
1050.175
1060.152
1070.014
1080.263
1090.399
110.458
1100.433
1110.902
1120.471
1130.787
1140.136
1150.322
1160.0275
1170.362
1180.922
1190.242
120.211
1200.434
1210.487
1220.0795
1230.739
1240.31
1250.519
1260.392
1270.959
1280.394
1290.343
130.856
1300.188
1310.552
1320.0637
1330.96
1340.655
1350.846
1360.945
1370.121
1380.857
1390.976
140.446
1400.509
1410.182
1420.318
1430.418
1440.608
1450.366
1460.178
1470.116
1480.658
1490.108
150.376
1500.342
1510.88
1520.0583
1530.511
1540.713
1550.103
1560.329
1570.476
1580.0452
1590.991
160.022
1600.202
1610.803
1620.458
1630.979
1640.0045
1650.731
1660.0412
1670.722
1680.701
1690.0103
170.593
180.559
190.00429
20.521
200.643
210.0512
220.615
230.596
240.243
250.461
260.125
270.889
280.612
290.743
30.266
300.764
310.578
329.21153e-23
330.926
340.995
350.984
360.539
370.0449
380.376
390.373
40.297
400.917
410.351
420.826
430.644
440.497
450.71
460.571
470.936
480.752
490.91
50.891
500.611
510.734
520.84
530.767
540.29
550.0434
560.894
570.315
580.558
590.252
60.522
600.812
610.681
620.559
630.194
640.893
650.691
660.0515
670.791
680.483
690.568
70.391
700.0427
710.212
720.346
730.0257
740.408
750.663
760.146
770.0868
780.76
791.42552e-4
80.116
800.0572
810.883
820.00562
830.472
840.639
850.194
860.807
870.851
880.121
890.293
90.687
900.936
910.965
920.0719
930.518
940.204
950.682
960.654
970.737
980.216
990.00131



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: CNhs13818


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

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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