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FF:11406-118E2: 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 17:07, 29 March 2012


Name:Small Airway 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
tissuelung
dev stage50 years old adult
sexmale
age50
cell typepneumocyte
cell lineNA
companyLonza
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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-penis0.131
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-0.424
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12016

Jaspar motifP-value
MA0002.20.00421
MA0003.10.831
MA0004.10.542
MA0006.10.043
MA0007.10.641
MA0009.10.209
MA0014.10.309
MA0017.10.183
MA0018.20.0725
MA0019.10.655
MA0024.14.23555e-5
MA0025.10.231
MA0027.10.679
MA0028.10.896
MA0029.10.145
MA0030.10.283
MA0031.10.77
MA0035.20.564
MA0038.10.0099
MA0039.20.0382
MA0040.10.516
MA0041.10.34
MA0042.10.835
MA0043.10.225
MA0046.10.829
MA0047.20.00275
MA0048.10.91
MA0050.11.87679e-8
MA0051.12.52678e-6
MA0052.10.00991
MA0055.10.219
MA0057.10.256
MA0058.10.172
MA0059.10.199
MA0060.14.28042e-5
MA0061.10.00426
MA0062.20.233
MA0065.20.306
MA0066.10.474
MA0067.10.215
MA0068.10.0556
MA0069.10.115
MA0070.10.927
MA0071.10.144
MA0072.10.416
MA0073.10.976
MA0074.10.728
MA0076.10.787
MA0077.10.377
MA0078.10.512
MA0079.20.0762
MA0080.26.2692e-10
MA0081.10.00237
MA0083.10.164
MA0084.10.278
MA0087.10.824
MA0088.10.0447
MA0090.10.0303
MA0091.10.0464
MA0092.10.0331
MA0093.10.473
MA0099.20.291
MA0100.10.0266
MA0101.10.0637
MA0102.20.0847
MA0103.11.74785e-8
MA0104.20.0826
MA0105.17.20503e-5
MA0106.13.18043e-8
MA0107.10.0329
MA0108.20.865
MA0111.10.316
MA0112.20.0655
MA0113.10.981
MA0114.10.209
MA0115.10.641
MA0116.10.00217
MA0117.10.556
MA0119.10.4
MA0122.10.373
MA0124.10.52
MA0125.10.178
MA0131.10.705
MA0135.10.268
MA0136.11.89665e-7
MA0137.20.0404
MA0138.20.52
MA0139.10.544
MA0140.10.669
MA0141.10.514
MA0142.10.13
MA0143.10.52
MA0144.10.67
MA0145.10.16
MA0146.10.429
MA0147.10.0546
MA0148.10.00507
MA0149.10.502
MA0150.10.366
MA0152.10.452
MA0153.10.45
MA0154.10.00704
MA0155.10.298
MA0156.12.50568e-4
MA0157.10.298
MA0159.10.966
MA0160.10.539
MA0162.10.718
MA0163.16.20361e-5
MA0164.10.812
MA0258.10.058
MA0259.10.94



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: CNhs12016

Novel motifP-value
10.38
100.0325
1000.168
1010.0789
1020.403
1030.375
1040.778
1050.619
1060.201
1070.234
1080.15
1090.372
110.426
1100.462
1110.562
1120.89
1130.661
1140.977
1150.111
1160.48
1170.539
1180.321
1190.93
120.632
1200.139
1210.323
1220.255
1230.179
1240.00303
1250.969
1260.815
1270.346
1280.882
1290.999
130.88
1300.0618
1310.812
1320.237
1330.00198
1340.0936
1350.553
1360.0034
1370.0246
1380.934
1390.186
140.877
1400.183
1410.324
1420.392
1430.11
1440.133
1450.325
1460.1
1470.267
1480.0377
1490.442
150.391
1500.537
1510.732
1520.00737
1530.378
1540.838
1550.426
1560.821
1570.762
1580.496
1590.71
160.523
1600.0664
1610.29
1620.502
1630.941
1640.372
1650.87
1660.392
1670.372
1680.65
1690.972
170.985
180.463
190.349
20.69
200.466
210.848
220.996
230.293
240.483
250.356
260.611
270.532
280.862
290.997
30.335
300.208
310.783
320.176
330.9
340.237
350.00322
360.0105
370.907
380.92
390.702
40.787
400.585
410.071
420.319
430.499
440.712
450.397
460.458
470.405
480.731
490.0338
50.396
500.74
510.616
520.175
530.029
540.803
550.579
560.868
570.945
580.442
590.895
60.0786
600.341
610.739
620.181
630.707
640.594
650.867
660.754
670.893
680.308
690.344
70.672
700.0301
710.078
720.808
730.0218
740.00499
750.539
760.788
770.68
780.325
790.916
80.477
800.0997
810.0614
820.367
830.211
840.475
850.383
860.756
870.0339
880.54
890.388
90.224
900.15
910.477
920.847
930.71
940.202
950.367
960.0488
970.816
980.125
990.695



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: CNhs12016


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)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002076 (endo-epithelial cell)
0002321 (embryonic cell)
0002368 (respiratory epithelial cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000065 (respiratory tract)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001004 (respiratory system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0005423 (developing anatomical structure)

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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