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FF:14317-155D6: 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 17:22, 29 March 2012


Name:Small Airway Epithelial Cells, donor3 (nuclear fraction)
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-penis0.0993
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-lymphoma0.36
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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: CNhs12583

Jaspar motifP-value
MA0002.23.953e-4
MA0003.10.137
MA0004.10.295
MA0006.10.884
MA0007.10.889
MA0009.10.348
MA0014.10.498
MA0017.10.0283
MA0018.20.0235
MA0019.10.423
MA0024.10.234
MA0025.10.995
MA0027.10.698
MA0028.12.80098e-5
MA0029.10.361
MA0030.10.62
MA0031.10.331
MA0035.20.0182
MA0038.10.576
MA0039.20.0161
MA0040.10.0325
MA0041.10.526
MA0042.10.429
MA0043.10.00654
MA0046.10.419
MA0047.20.0696
MA0048.10.139
MA0050.10.00284
MA0051.10.0215
MA0052.10.129
MA0055.10.0053
MA0057.10.872
MA0058.10.23
MA0059.10.164
MA0060.10.0805
MA0061.10.0326
MA0062.23.0954e-7
MA0065.20.00412
MA0066.10.0215
MA0067.10.623
MA0068.10.187
MA0069.10.221
MA0070.10.187
MA0071.10.065
MA0072.10.371
MA0073.10.928
MA0074.10.12
MA0076.15.69472e-6
MA0077.10.834
MA0078.10.61
MA0079.20.264
MA0080.20.208
MA0081.10.821
MA0083.10.991
MA0084.10.976
MA0087.10.312
MA0088.10.932
MA0090.10.0171
MA0091.10.00142
MA0092.10.072
MA0093.10.309
MA0099.20.00386
MA0100.10.855
MA0101.10.706
MA0102.20.602
MA0103.10.81
MA0104.20.376
MA0105.11.55696e-5
MA0106.12.05124e-7
MA0107.10.297
MA0108.20.313
MA0111.10.863
MA0112.21.38913e-4
MA0113.10.5
MA0114.10.128
MA0115.10.405
MA0116.14.26451e-4
MA0117.10.811
MA0119.10.438
MA0122.10.965
MA0124.10.972
MA0125.10.133
MA0131.10.0364
MA0135.10.493
MA0136.10.0139
MA0137.20.16
MA0138.20.0222
MA0139.10.133
MA0140.10.112
MA0141.10.00675
MA0142.10.896
MA0143.10.337
MA0144.10.848
MA0145.10.898
MA0146.10.597
MA0147.10.501
MA0148.10.136
MA0149.10.281
MA0150.10.695
MA0152.10.611
MA0153.10.621
MA0154.10.00132
MA0155.10.0744
MA0156.14.0112e-4
MA0157.10.323
MA0159.10.0404
MA0160.10.0784
MA0162.10.384
MA0163.14.91501e-5
MA0164.10.881
MA0258.10.00104
MA0259.10.869



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: CNhs12583

Novel motifP-value
10.137
100.139
1000.994
1010.482
1020.725
1030.159
1040.842
1050.919
1060.011
1070.168
1080.441
1090.502
110.0887
1100.642
1110.681
1120.214
1130.945
1140.103
1150.123
1160.162
1170.977
1180.676
1190.254
120.457
1200.653
1210.57
1220.88
1230.737
1240.0173
1250.31
1260.521
1270.44
1280.0194
1290.515
130.874
1300.244
1310.473
1320.668
1330.00237
1340.258
1350.0552
1360.334
1370.171
1380.817
1390.00693
140.903
1400.321
1410.631
1420.132
1430.00273
1440.186
1450.892
1460.951
1470.878
1480.0118
1490.0176
150.0274
1500.641
1510.513
1520.871
1530.875
1540.968
1550.753
1560.65
1570.536
1580.599
1590.343
160.219
1600.0246
1610.28
1620.904
1630.991
1640.983
1650.665
1660.721
1670.654
1680.526
1690.061
170.231
180.0145
190.0278
20.412
200.24
210.273
220.198
230.252
240.989
250.247
260.689
270.043
280.52
290.684
30.513
300.965
310.414
320.00379
330.985
340.303
350.0322
360.305
370.339
380.662
390.703
40.655
400.374
410.0787
420.643
430.133
440.00394
450.885
460.0505
470.278
480.608
490.0938
50.159
500.634
510.189
520.469
530.463
540.205
550.918
560.508
570.674
580.206
590.0185
60.725
600.145
610.416
620.0309
630.669
640.122
650.135
660.912
670.637
680.67
690.0853
70.507
700.148
710.237
720.376
730.961
740.0138
750.365
760.369
770.147
780.955
790.0148
80.0277
800.152
810.0688
820.0418
830.0575
840.862
850.0334
860.368
870.769
880.444
890.0539
90.136
900.54
910.383
920.0552
930.718
940.0377
950.625
960.209
970.66
980.0969
990.936



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: CNhs12583


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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