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FF:11933-125I7: 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, donor1
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
age59
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-penis0.0363
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-0.285
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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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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: CNhs13816

Jaspar motifP-value
MA0002.20.0128
MA0003.10.57
MA0004.10.135
MA0006.10.367
MA0007.10.804
MA0009.10.473
MA0014.10.397
MA0017.10.0723
MA0018.22.90522e-6
MA0019.10.224
MA0024.12.55127e-4
MA0025.10.00223
MA0027.10.499
MA0028.10.0032
MA0029.10.655
MA0030.10.0259
MA0031.10.118
MA0035.20.00527
MA0038.10.00602
MA0039.20.00361
MA0040.10.437
MA0041.10.247
MA0042.10.75
MA0043.13.36081e-5
MA0046.10.261
MA0047.20.15
MA0048.10.00182
MA0050.10.805
MA0051.10.867
MA0052.10.142
MA0055.10.92
MA0057.10.245
MA0058.10.00846
MA0059.10.544
MA0060.19.93454e-15
MA0061.10.131
MA0062.29.07563e-11
MA0065.20.588
MA0066.10.481
MA0067.10.00462
MA0068.10.65
MA0069.10.283
MA0070.10.601
MA0071.10.981
MA0072.10.159
MA0073.10.198
MA0074.10.224
MA0076.14.27733e-5
MA0077.10.802
MA0078.10.939
MA0079.20.192
MA0080.21.95156e-8
MA0081.10.00122
MA0083.10.00325
MA0084.10.0761
MA0087.10.966
MA0088.10.185
MA0090.10.00292
MA0091.10.0244
MA0092.10.179
MA0093.10.0612
MA0099.22.47738e-6
MA0100.10.204
MA0101.10.02
MA0102.20.4
MA0103.10.063
MA0104.20.00873
MA0105.10.403
MA0106.10.317
MA0107.10.0225
MA0108.20.177
MA0111.10.431
MA0112.20.0111
MA0113.10.573
MA0114.10.178
MA0115.10.0277
MA0116.10.706
MA0117.10.0616
MA0119.10.0109
MA0122.10.107
MA0124.10.868
MA0125.10.577
MA0131.10.937
MA0135.10.0689
MA0136.18.37152e-12
MA0137.20.0139
MA0138.20.686
MA0139.10.555
MA0140.10.00622
MA0141.10.94
MA0142.10.329
MA0143.10.853
MA0144.10.472
MA0145.10.957
MA0146.10.378
MA0147.10.0353
MA0148.10.176
MA0149.10.932
MA0150.10.0106
MA0152.10.0187
MA0153.10.173
MA0154.10.975
MA0155.10.575
MA0156.14.01293e-11
MA0157.10.123
MA0159.10.722
MA0160.10.0687
MA0162.10.0244
MA0163.10.0479
MA0164.10.86
MA0258.10.173
MA0259.10.452



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: CNhs13816

Novel motifP-value
10.908
100.571
1000.485
1010.803
1020.209
1030.744
1040.749
1050.178
1060.0104
1070.0124
1080.18
1090.771
110.456
1100.54
1110.904
1120.404
1130.634
1140.252
1150.139
1160.0237
1170.556
1180.998
1190.15
120.158
1200.301
1210.554
1220.0758
1230.571
1240.244
1250.457
1260.433
1270.686
1280.0654
1290.53
130.962
1300.252
1310.421
1320.0748
1330.972
1340.861
1350.832
1360.951
1370.075
1380.597
1390.459
140.519
1400.756
1410.175
1420.183
1430.646
1440.519
1450.317
1460.146
1470.275
1480.753
1490.0561
150.334
1500.168
1510.979
1520.0464
1530.522
1540.917
1550.484
1560.477
1570.391
1580.187
1590.773
160.0364
1600.334
1610.939
1620.834
1630.747
1640.00897
1650.462
1660.0255
1670.717
1680.571
1690.024
170.423
180.426
190.00304
20.244
200.967
210.0572
220.541
230.338
240.124
250.269
260.139
270.981
280.55
290.575
30.296
300.537
310.461
327.4432e-23
330.568
340.878
350.775
360.135
370.145
380.508
390.346
40.312
400.466
410.324
420.703
430.729
440.264
450.811
460.279
470.924
480.588
490.8
50.821
500.497
510.701
520.666
530.656
540.365
550.0797
560.79
570.544
580.603
590.289
60.408
600.7
610.963
620.588
630.167
640.845
650.333
660.0244
670.589
680.362
690.26
70.302
700.0676
710.363
720.26
730.0507
740.592
750.641
760.364
770.115
780.957
793.48209e-5
80.188
800.0457
810.899
820.0156
830.515
840.627
850.0278
860.77
870.638
880.109
890.315
90.681
900.852
910.565
920.132
930.856
940.328
950.97
960.744
970.832
980.392
990.0125



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: CNhs13816


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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