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FF:11934-125I8: 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, donor2
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
sexfemale
age66
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-penis0.0938
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-0.0671
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs13817

Jaspar motifP-value
MA0002.20.0953
MA0003.10.764
MA0004.10.221
MA0006.10.37
MA0007.10.988
MA0009.10.531
MA0014.10.51
MA0017.10.42
MA0018.23.10456e-6
MA0019.10.421
MA0024.10.00146
MA0025.14.84061e-4
MA0027.10.85
MA0028.10.0162
MA0029.10.631
MA0030.10.00128
MA0031.10.0241
MA0035.20.00848
MA0038.10.00672
MA0039.20.0102
MA0040.10.566
MA0041.10.179
MA0042.10.656
MA0043.19.14806e-6
MA0046.10.0298
MA0047.20.0544
MA0048.10.00709
MA0050.10.241
MA0051.10.459
MA0052.10.022
MA0055.10.984
MA0057.10.0856
MA0058.10.0236
MA0059.10.94
MA0060.13.83235e-12
MA0061.10.433
MA0062.24.8409e-8
MA0065.20.397
MA0066.10.242
MA0067.10.00549
MA0068.10.274
MA0069.10.171
MA0070.10.576
MA0071.10.98
MA0072.10.241
MA0073.10.563
MA0074.10.264
MA0076.13.42068e-4
MA0077.10.823
MA0078.10.829
MA0079.20.103
MA0080.21.17755e-7
MA0081.10.00722
MA0083.10.376
MA0084.10.162
MA0087.10.741
MA0088.10.467
MA0090.10.011
MA0091.10.0428
MA0092.10.201
MA0093.10.115
MA0099.26.05743e-5
MA0100.10.333
MA0101.10.0112
MA0102.20.196
MA0103.10.459
MA0104.20.0848
MA0105.10.271
MA0106.10.0396
MA0107.10.0117
MA0108.20.00656
MA0111.10.894
MA0112.25.98933e-4
MA0113.10.517
MA0114.10.508
MA0115.10.154
MA0116.10.035
MA0117.10.193
MA0119.10.00181
MA0122.10.379
MA0124.10.409
MA0125.10.229
MA0131.10.43
MA0135.10.165
MA0136.11.17521e-10
MA0137.20.00474
MA0138.20.502
MA0139.10.474
MA0140.10.00695
MA0141.10.538
MA0142.10.219
MA0143.10.91
MA0144.10.378
MA0145.10.686
MA0146.10.285
MA0147.10.364
MA0148.10.111
MA0149.10.413
MA0150.10.0227
MA0152.10.0846
MA0153.10.107
MA0154.10.282
MA0155.10.334
MA0156.11.16353e-10
MA0157.10.111
MA0159.10.291
MA0160.10.129
MA0162.10.0527
MA0163.15.95846e-5
MA0164.10.979
MA0258.10.0232
MA0259.10.658



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: CNhs13817

Novel motifP-value
10.273
100.0928
1000.63
1010.843
1020.245
1030.601
1040.846
1050.118
1060.0201
1070.0278
1080.192
1090.293
110.214
1100.266
1110.528
1120.236
1130.841
1140.0225
1150.0122
1160.036
1170.295
1180.511
1190.164
120.21
1200.0711
1210.752
1220.063
1230.525
1240.273
1250.342
1260.521
1270.96
1280.193
1290.837
130.701
1300.152
1310.525
1320.138
1330.95
1340.665
1350.935
1360.634
1370.186
1380.922
1390.765
140.345
1400.89
1410.5
1420.263
1430.819
1440.656
1450.365
1460.126
1470.249
1480.647
1490.0378
150.813
1500.298
1510.704
1520.0527
1530.716
1540.487
1550.407
1560.353
1570.32
1580.0575
1590.743
160.0105
1600.125
1610.741
1620.447
1630.975
1640.0214
1650.865
1660.0442
1670.897
1680.549
1690.00543
170.305
180.346
190.00209
20.466
200.772
210.0267
220.497
230.437
240.428
250.555
260.121
270.607
280.562
290.327
30.317
300.893
310.526
321.18936e-19
330.805
340.776
350.46
360.258
370.0327
380.507
390.292
40.455
400.858
410.536
420.69
430.469
440.044
450.707
460.132
470.56
480.479
490.951
50.864
500.816
510.78
520.878
530.568
540.379
550.204
560.828
570.561
580.767
590.0818
60.496
600.727
610.908
620.334
630.196
640.748
650.566
660.0645
670.726
680.563
690.266
70.487
700.115
710.0681
720.44
730.0302
740.479
750.157
760.497
770.0278
780.985
791.70911e-6
80.0622
800.0478
810.845
820.0136
830.413
840.404
850.03
860.705
870.567
880.174
890.143
90.969
900.994
910.583
920.21
930.86
940.176
950.258
960.894
970.967
980.434
990.00716



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: CNhs13817


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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