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FF:11457-119A8: 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 17:09, 29 March 2012


Name:Bronchial Epithelial Cell, donor5
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 stage63 years old adult
sexfemale
age63
cell typeepithelial cell of lung, bronchial
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1473
catalog numberCA502-R10a
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-0.0792
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-0.00803
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
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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: CNhs12058

Jaspar motifP-value
MA0002.20.878
MA0003.10.381
MA0004.10.945
MA0006.10.103
MA0007.10.163
MA0009.10.199
MA0014.10.631
MA0017.10.171
MA0018.20.466
MA0019.10.252
MA0024.10.777
MA0025.10.513
MA0027.10.278
MA0028.10.501
MA0029.10.106
MA0030.10.593
MA0031.10.0308
MA0035.20.0576
MA0038.10.428
MA0039.20.00387
MA0040.10.564
MA0041.10.364
MA0042.10.937
MA0043.10.578
MA0046.10.243
MA0047.20.569
MA0048.10.452
MA0050.11.01063e-9
MA0051.17.84296e-5
MA0052.10.573
MA0055.17.206e-4
MA0057.10.0517
MA0058.10.725
MA0059.10.399
MA0060.10.00142
MA0061.10.864
MA0062.20.367
MA0065.20.0354
MA0066.10.113
MA0067.10.209
MA0068.10.0313
MA0069.10.884
MA0070.10.199
MA0071.10.874
MA0072.10.768
MA0073.10.671
MA0074.10.692
MA0076.10.949
MA0077.10.425
MA0078.10.411
MA0079.20.22
MA0080.20.0682
MA0081.10.197
MA0083.10.823
MA0084.10.127
MA0087.10.621
MA0088.10.465
MA0090.10.0214
MA0091.10.843
MA0092.10.702
MA0093.10.843
MA0099.25.59633e-15
MA0100.10.0237
MA0101.10.801
MA0102.20.029
MA0103.18.31468e-6
MA0104.20.974
MA0105.10.862
MA0106.16.60975e-7
MA0107.10.896
MA0108.20.00119
MA0111.10.554
MA0112.20.127
MA0113.10.185
MA0114.10.0909
MA0115.10.154
MA0116.10.423
MA0117.10.406
MA0119.10.615
MA0122.10.386
MA0124.10.929
MA0125.10.378
MA0131.10.397
MA0135.10.0421
MA0136.10.929
MA0137.20.0146
MA0138.20.204
MA0139.10.767
MA0140.10.697
MA0141.10.271
MA0142.10.0881
MA0143.10.715
MA0144.10.651
MA0145.10.053
MA0146.10.0151
MA0147.10.807
MA0148.10.443
MA0149.10.0622
MA0150.10.298
MA0152.10.0995
MA0153.10.0983
MA0154.10.331
MA0155.10.289
MA0156.10.559
MA0157.10.0385
MA0159.10.861
MA0160.10.217
MA0162.10.124
MA0163.10.705
MA0164.10.683
MA0258.10.326
MA0259.10.996



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: CNhs12058

Novel motifP-value
10.909
100.398
1000.294
1010.0013
1020.305
1030.379
1040.276
1050.0765
1060.0733
1070.0812
1080.588
1090.0012
110.109
1100.128
1110.586
1120.77
1130.292
1140.841
1150.214
1160.507
1170.491
1180.858
1190.299
120.223
1200.207
1210.293
1220.0231
1230.166
1240.155
1250.381
1260.741
1270.229
1280.53
1290.135
130.0509
1300.204
1310.418
1320.278
1330.00161
1340.362
1350.987
1360.0722
1370.0506
1380.737
1390.815
140.827
1400.865
1410.948
1420.0376
1430.919
1440.155
1450.388
1460.011
1470.126
1480.125
1490.814
150.713
1500.249
1510.495
1520.0336
1530.475
1540.446
1550.449
1560.433
1570.798
1580.189
1590.929
160.28
1600.137
1610.149
1620.13
1630.864
1640.959
1650.375
1660.409
1670.0781
1680.997
1690.0762
170.16
180.64
190.655
20.109
200.971
210.837
220.102
230.591
240.275
250.729
260.0714
270.317
280.858
290.62
30.856
300.0352
310.685
320.479
330.16
340.514
350.207
360.704
370.345
380.296
390.382
40.274
400.00233
410.876
420.992
430.919
440.786
450.124
460.6
470.45
480.0882
490.604
50.302
500.416
510.947
520.348
530.493
540.777
550.444
560.489
570.728
580.724
590.0613
60.307
600.299
610.677
620.546
630.271
640.302
650.274
660.25
670.218
680.579
690.202
70.452
700.146
710.533
720.61
730.0107
740.0343
750.467
760.456
770.00781
780.18
790.641
80.305
800.638
810.161
820.798
830.823
840.806
850.624
860.919
870.00864
880.613
890.197
90.666
900.00278
910.895
920.576
930.787
940.504
950.0174
960.545
970.799
980.362
990.0178



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: CNhs12058


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)
0000082 (epithelial cell of lung)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002076 (endo-epithelial cell)
0002202 (epithelial cell of tracheobronchial tree)
0002321 (embryonic cell)
0002328 (bronchial epithelial cell)
0002368 (respiratory epithelial cell)
0002371 (somatic cell)
0002632 (epithelial cell of lower respiratory tract)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000115 (lung epithelium)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000485 (simple columnar epithelium)
0000490 (unilaminar epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001558 (lower respiratory tract)
0002031 (epithelium of bronchus)
0002048 (lung)
0002050 (embryonic structure)
0002185 (bronchus)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004802 (respiratory tract epithelium)
0004807 (respiratory system epithelium)
0004815 (lower respiratory tract epithelium)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0007026 (primitive gut)
0007196 (tracheobronchial tree)
0008947 (respiratory primordium)
0009142 (entire embryonic mesenchyme)

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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