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FF:11461-119B3: 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 17:10, 29 March 2012


Name:Bronchial Epithelial Cell, donor6
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 stage45 years old adult
sexmale
age45
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 number1217
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-0.0602
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-0.237
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



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: CNhs12062

Jaspar motifP-value
MA0002.20.997
MA0003.10.421
MA0004.10.533
MA0006.10.146
MA0007.10.209
MA0009.10.198
MA0014.10.423
MA0017.10.137
MA0018.20.197
MA0019.10.608
MA0024.10.00499
MA0025.10.446
MA0027.10.425
MA0028.10.0564
MA0029.10.26
MA0030.10.969
MA0031.10.0757
MA0035.20.266
MA0038.10.528
MA0039.20.00513
MA0040.10.666
MA0041.10.346
MA0042.10.978
MA0043.10.354
MA0046.10.351
MA0047.20.0929
MA0048.10.665
MA0050.13.69934e-11
MA0051.15.18939e-6
MA0052.10.853
MA0055.10.0107
MA0057.10.0965
MA0058.10.312
MA0059.10.619
MA0060.10.239
MA0061.10.779
MA0062.20.0679
MA0065.20.00905
MA0066.10.116
MA0067.10.231
MA0068.10.0323
MA0069.10.55
MA0070.10.952
MA0071.10.937
MA0072.10.963
MA0073.10.784
MA0074.10.98
MA0076.10.262
MA0077.10.951
MA0078.10.616
MA0079.20.28
MA0080.20.0562
MA0081.10.229
MA0083.10.467
MA0084.10.0817
MA0087.10.409
MA0088.10.435
MA0090.10.0656
MA0091.10.83
MA0092.10.934
MA0093.10.466
MA0099.26.66228e-14
MA0100.10.0475
MA0101.10.725
MA0102.20.55
MA0103.13.67011e-7
MA0104.20.851
MA0105.10.797
MA0106.17.77906e-8
MA0107.10.587
MA0108.20.191
MA0111.10.811
MA0112.20.0237
MA0113.10.312
MA0114.10.07
MA0115.10.628
MA0116.10.121
MA0117.10.596
MA0119.10.275
MA0122.10.553
MA0124.10.611
MA0125.10.664
MA0131.10.41
MA0135.10.0334
MA0136.10.563
MA0137.20.00988
MA0138.20.096
MA0139.10.366
MA0140.10.923
MA0141.10.0801
MA0142.10.221
MA0143.10.771
MA0144.10.632
MA0145.10.0299
MA0146.10.0237
MA0147.10.994
MA0148.10.0548
MA0149.10.122
MA0150.10.109
MA0152.10.147
MA0153.10.19
MA0154.10.222
MA0155.10.322
MA0156.10.6
MA0157.10.0355
MA0159.10.0768
MA0160.10.302
MA0162.10.165
MA0163.10.404
MA0164.10.885
MA0258.10.122
MA0259.10.803



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: CNhs12062

Novel motifP-value
10.579
100.976
1000.737
1010.00153
1020.0949
1030.151
1040.392
1050.0888
1060.0502
1070.0716
1080.44
1095.50129e-4
110.0631
1100.0716
1110.502
1120.243
1130.433
1140.349
1150.163
1160.274
1170.174
1180.908
1190.142
120.32
1200.0762
1210.741
1220.07
1230.379
1240.132
1250.848
1260.495
1270.0344
1280.612
1290.121
130.0349
1300.773
1310.427
1320.489
1335.7783e-4
1340.189
1350.976
1360.0753
1370.0702
1380.704
1390.233
140.736
1400.0489
1410.421
1420.0492
1430.508
1440.233
1450.368
1460.00567
1470.0425
1480.18
1490.191
150.893
1500.349
1510.494
1520.036
1530.995
1540.596
1550.438
1560.305
1570.701
1580.388
1590.597
160.0202
1600.313
1610.395
1620.39
1630.699
1640.271
1650.235
1660.13
1670.264
1680.768
1690.0502
170.14
180.0569
190.404
20.175
200.717
210.476
220.187
230.58
240.109
250.81
260.143
270.448
280.762
290.238
30.582
300.0711
310.696
320.676
330.128
340.808
350.663
360.738
370.166
380.317
390.23
40.531
400.00877
410.659
420.966
430.446
440.582
450.205
460.411
470.181
480.069
490.988
50.66
500.522
510.761
520.491
530.386
540.575
550.929
560.376
570.532
580.988
590.056
60.186
600.23
610.616
620.898
630.259
640.239
650.161
660.734
670.599
680.809
690.141
70.527
700.00644
710.262
720.956
730.0127
740.0261
750.145
760.916
770.00456
780.0568
790.544
80.246
800.984
810.585
820.681
830.513
840.899
850.492
860.785
870.00589
880.473
890.0912
90.672
900.133
910.617
920.74
930.666
940.686
950.031
960.53
970.726
980.36
990.0205



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: CNhs12062


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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