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FF:12226-129F3: 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 17:23, 29 March 2012


Name:nasal 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
tissuenasal cavity
dev stageNA
sexNA
ageNA
cell typeepithelial cell
cell lineNA
companyPromocell
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
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-0.117
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-0.445
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



No results for this sample



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: CNhs12589

Jaspar motifP-value
MA0002.20.385
MA0003.10.997
MA0004.10.259
MA0006.10.283
MA0007.10.985
MA0009.10.0703
MA0014.10.0479
MA0017.10.859
MA0018.20.824
MA0019.10.913
MA0024.16.15893e-5
MA0025.10.0399
MA0027.10.662
MA0028.11.39718e-6
MA0029.10.323
MA0030.10.604
MA0031.10.175
MA0035.20.268
MA0038.10.293
MA0039.22.70979e-4
MA0040.10.275
MA0041.10.377
MA0042.10.83
MA0043.10.0139
MA0046.10.381
MA0047.20.0348
MA0048.10.932
MA0050.12.85789e-14
MA0051.13.86313e-6
MA0052.10.241
MA0055.10.00169
MA0057.10.112
MA0058.10.289
MA0059.10.177
MA0060.10.0774
MA0061.10.318
MA0062.26.47929e-5
MA0065.20.105
MA0066.10.8
MA0067.10.706
MA0068.10.024
MA0069.10.307
MA0070.10.944
MA0071.10.938
MA0072.10.708
MA0073.10.727
MA0074.10.401
MA0076.11.94079e-4
MA0077.10.999
MA0078.10.817
MA0079.20.618
MA0080.23.95928e-6
MA0081.10.263
MA0083.10.919
MA0084.10.0771
MA0087.10.364
MA0088.10.199
MA0090.10.0276
MA0091.10.0826
MA0092.10.935
MA0093.10.29
MA0099.21.31813e-8
MA0100.10.0215
MA0101.10.281
MA0102.20.133
MA0103.12.90141e-10
MA0104.20.0815
MA0105.10.437
MA0106.13.49233e-9
MA0107.10.184
MA0108.20.882
MA0111.10.884
MA0112.20.638
MA0113.10.321
MA0114.10.179
MA0115.10.679
MA0116.10.607
MA0117.10.638
MA0119.10.388
MA0122.10.944
MA0124.10.917
MA0125.10.0438
MA0131.10.69
MA0135.10.363
MA0136.10.0318
MA0137.20.129
MA0138.20.947
MA0139.10.397
MA0140.10.498
MA0141.10.623
MA0142.10.508
MA0143.10.809
MA0144.10.903
MA0145.10.0139
MA0146.10.282
MA0147.10.1
MA0148.10.0127
MA0149.10.0524
MA0150.10.325
MA0152.10.294
MA0153.10.809
MA0154.10.785
MA0155.10.342
MA0156.10.642
MA0157.10.155
MA0159.10.0331
MA0160.10.225
MA0162.10.341
MA0163.10.746
MA0164.10.561
MA0258.10.555
MA0259.10.543


library id: CNhs12554This sample isn't target for the analysis



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: CNhs12589

Novel motifP-value
10.374
100.843
1000.774
1010.242
1020.257
1030.242
1040.7
1050.0151
1060.637
1070.766
1080.218
1095.01831e-4
110.285
1100.144
1110.137
1120.346
1130.0666
1140.401
1150.614
1160.52
1170.216
1180.917
1190.537
120.6
1200.187
1210.536
1220.0147
1230.958
1240.175
1250.589
1260.167
1270.102
1280.912
1290.498
130.0056
1300.458
1310.652
1320.783
1330.0041
1340.518
1350.996
1360.0707
1370.23
1380.508
1390.11
140.599
1400.274
1410.784
1420.355
1430.576
1440.0675
1450.303
1460.0118
1470.706
1480.0616
1490.868
150.295
1500.772
1510.438
1520.0665
1530.183
1540.899
1550.819
1560.914
1570.83
1580.956
1590.323
160.102
1600.932
1610.893
1620.891
1630.537
1640.0882
1650.971
1660.441
1670.78
1680.753
1690.173
170.244
180.0951
190.697
20.733
200.245
210.828
220.526
230.481
240.11
250.875
260.453
270.658
280.549
290.149
30.49
300.316
310.856
320.137
330.154
340.507
350.261
360.207
370.179
380.335
390.536
40.615
400.00611
410.244
420.473
430.415
440.835
450.256
460.848
470.255
480.251
490.648
50.89
500.47
510.932
520.552
530.554
540.723
550.981
560.557
570.15
580.878
590.506
60.49
600.308
610.25
620.77
630.139
640.302
650.341
660.559
670.5
680.0397
690.343
70.189
700.0032
710.572
720.17
730.00971
740.0895
750.162
760.393
770.171
780.00643
790.0888
80.671
800.621
810.516
820.781
830.486
840.8
850.429
860.806
870.00983
880.872
890.0298
90.656
900.709
910.631
920.491
930.375
940.736
950.0135
960.424
970.787
980.581
990.432


library id: CNhs12554This sample isn't target for the analysis



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: CNhs12589
library id: CNhs12554


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)
0000075 (columnar/cuboidal epithelial cell)
0000098 (sensory epithelial cell)
0000133 (neurectodermal cell)
0000197 (receptor cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000710 (neurecto-epithelial cell)
0002077 (ecto-epithelial cell)
0002167 (olfactory epithelial cell)
0002321 (embryonic cell)
0002371 (somatic cell)

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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