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FF:11256-116F5: 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 16:37, 29 March 2012


Name:Small Airway 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
tissuelung
dev stage19 years old adult
sexfemale
age19
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-penis-0.0229
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-0.351
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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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: CNhs10884

Jaspar motifP-value
MA0002.20.435
MA0003.10.636
MA0004.10.108
MA0006.10.0307
MA0007.10.596
MA0009.10.339
MA0014.10.185
MA0017.10.905
MA0018.26.63592e-4
MA0019.10.33
MA0024.17.89445e-7
MA0025.10.589
MA0027.10.689
MA0028.10.017
MA0029.10.288
MA0030.10.601
MA0031.10.577
MA0035.20.713
MA0038.10.00182
MA0039.20.00497
MA0040.10.166
MA0041.10.661
MA0042.10.501
MA0043.10.901
MA0046.10.894
MA0047.20.0316
MA0048.10.938
MA0050.13.84718e-8
MA0051.11.81847e-4
MA0052.10.00334
MA0055.10.154
MA0057.10.0423
MA0058.10.0296
MA0059.10.752
MA0060.11.35903e-9
MA0061.10.613
MA0062.20.269
MA0065.20.0884
MA0066.10.212
MA0067.10.0555
MA0068.10.00727
MA0069.10.183
MA0070.10.424
MA0071.10.244
MA0072.10.469
MA0073.10.714
MA0074.10.76
MA0076.10.205
MA0077.10.954
MA0078.10.862
MA0079.20.376
MA0080.20.00145
MA0081.10.166
MA0083.10.0446
MA0084.10.219
MA0087.10.652
MA0088.10.795
MA0090.10.00184
MA0091.10.305
MA0092.10.89
MA0093.10.0689
MA0099.25.20806e-5
MA0100.10.12
MA0101.10.224
MA0102.20.508
MA0103.12.10649e-8
MA0104.20.338
MA0105.10.731
MA0106.19.7644e-12
MA0107.10.269
MA0108.20.0329
MA0111.10.709
MA0112.20.0945
MA0113.10.714
MA0114.10.661
MA0115.10.628
MA0116.10.201
MA0117.10.63
MA0119.10.447
MA0122.10.734
MA0124.10.75
MA0125.10.13
MA0131.10.65
MA0135.10.431
MA0136.10.0589
MA0137.20.144
MA0138.20.632
MA0139.10.24
MA0140.10.467
MA0141.10.94
MA0142.10.701
MA0143.10.556
MA0144.10.947
MA0145.10.0076
MA0146.10.212
MA0147.10.535
MA0148.10.00649
MA0149.10.12
MA0150.10.855
MA0152.10.553
MA0153.10.296
MA0154.10.55
MA0155.10.656
MA0156.10.359
MA0157.10.221
MA0159.10.0128
MA0160.10.621
MA0162.10.142
MA0163.10.606
MA0164.10.636
MA0258.10.816
MA0259.10.673



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: CNhs10884

Novel motifP-value
10.538
100.736
1000.771
1010.217
1020.397
1030.035
1040.912
1050.764
1060.0372
1070.123
1080.195
1090.00188
110.399
1100.28
1110.167
1120.143
1130.564
1140.107
1150.379
1160.987
1170.243
1180.801
1190.394
120.415
1200.00998
1210.411
1220.453
1230.282
1240.0637
1250.131
1260.708
1270.339
1280.631
1290.187
130.0542
1300.0603
1310.722
1320.164
1337.46865e-4
1340.318
1350.912
1360.01
1370.056
1380.572
1390.0729
140.822
1400.323
1410.549
1420.548
1430.58
1440.235
1450.945
1460.123
1470.116
1480.685
1490.345
150.877
1500.282
1510.336
1520.00483
1530.331
1540.982
1550.814
1560.969
1570.814
1580.195
1590.561
160.00261
1600.689
1610.898
1620.635
1630.898
1640.191
1650.946
1660.36
1670.718
1680.595
1690.0778
170.376
180.221
190.746
20.23
200.801
210.293
220.648
230.237
240.00914
250.994
260.939
270.545
280.713
290.137
30.414
300.272
310.743
320.795
330.0557
340.265
350.371
360.679
370.0823
380.608
390.283
40.825
400.164
410.14
420.609
430.526
440.231
450.265
460.644
470.248
480.131
490.452
50.936
500.593
510.836
520.28
530.162
540.755
550.206
560.538
570.52
580.645
590.273
60.441
600.192
610.703
620.657
630.177
640.663
650.669
660.898
670.395
680.133
690.517
70.592
700.00206
710.214
720.435
730.00148
740.0918
750.152
760.659
770.04
780.0304
790.996
80.37
800.72
810.538
820.588
830.642
840.556
850.248
860.878
870.00721
880.793
890.0438
90.397
900.989
910.589
920.515
930.461
940.775
950.0462
960.552
970.892
980.359
990.238



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: CNhs10884


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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