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FF:11453-119A4: 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, donor4
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 stage20 years old adult
sexmale
age20
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 number1858
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-0.169
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-lymphoma0.158
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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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: CNhs12054

Jaspar motifP-value
MA0002.20.789
MA0003.10.328
MA0004.10.817
MA0006.10.303
MA0007.10.181
MA0009.10.0448
MA0014.10.46
MA0017.10.0183
MA0018.20.25
MA0019.10.221
MA0024.10.633
MA0025.10.409
MA0027.10.481
MA0028.10.0187
MA0029.10.248
MA0030.10.423
MA0031.10.0113
MA0035.20.111
MA0038.10.241
MA0039.20.00368
MA0040.10.286
MA0041.10.403
MA0042.10.871
MA0043.10.389
MA0046.10.528
MA0047.20.536
MA0048.10.617
MA0050.11.27383e-9
MA0051.17.93155e-4
MA0052.10.971
MA0055.10.0015
MA0057.10.0514
MA0058.10.627
MA0059.10.164
MA0060.10.0129
MA0061.10.592
MA0062.20.00456
MA0065.20.00257
MA0066.10.108
MA0067.10.139
MA0068.10.00388
MA0069.10.529
MA0070.10.886
MA0071.10.936
MA0072.10.912
MA0073.10.531
MA0074.10.934
MA0076.10.107
MA0077.10.577
MA0078.10.682
MA0079.20.712
MA0080.20.121
MA0081.10.597
MA0083.10.391
MA0084.10.0318
MA0087.10.348
MA0088.10.0763
MA0090.10.0251
MA0091.10.951
MA0092.10.451
MA0093.10.747
MA0099.23.98096e-13
MA0100.10.0646
MA0101.10.755
MA0102.20.0296
MA0103.12.13766e-6
MA0104.20.428
MA0105.10.514
MA0106.12.32738e-6
MA0107.10.937
MA0108.20.00513
MA0111.10.901
MA0112.20.0241
MA0113.10.737
MA0114.10.0187
MA0115.10.486
MA0116.10.0787
MA0117.10.957
MA0119.10.398
MA0122.10.89
MA0124.10.89
MA0125.10.218
MA0131.10.627
MA0135.10.0521
MA0136.10.458
MA0137.20.339
MA0138.20.169
MA0139.10.556
MA0140.10.273
MA0141.10.0945
MA0142.10.00695
MA0143.10.837
MA0144.10.98
MA0145.10.0639
MA0146.10.0464
MA0147.10.256
MA0148.10.394
MA0149.10.0332
MA0150.10.223
MA0152.10.225
MA0153.10.0697
MA0154.10.232
MA0155.10.607
MA0156.10.147
MA0157.10.144
MA0159.10.116
MA0160.10.089
MA0162.10.0717
MA0163.10.147
MA0164.10.62
MA0258.10.166
MA0259.10.431



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: CNhs12054

Novel motifP-value
10.434
100.77
1000.183
1010.00547
1020.28
1030.219
1040.575
1050.163
1060.264
1070.344
1080.837
1091.58616e-4
110.0463
1100.0168
1110.594
1120.63
1130.528
1140.45
1150.333
1160.142
1170.175
1180.688
1190.212
120.303
1200.06
1210.38
1220.0166
1230.56
1240.566
1250.676
1260.437
1270.107
1280.983
1290.114
130.00426
1300.414
1310.253
1320.602
1330.0029
1340.191
1350.769
1360.0956
1370.378
1380.968
1390.718
140.941
1400.91
1410.966
1420.0592
1430.923
1440.123
1450.852
1460.0113
1470.141
1480.618
1490.949
150.635
1500.539
1510.518
1520.111
1530.597
1540.312
1550.402
1560.276
1570.731
1580.316
1590.795
160.153
1600.0854
1610.0894
1620.625
1630.481
1640.467
1650.647
1660.57
1670.719
1680.518
1690.0716
170.112
180.525
190.806
20.126
200.971
210.973
220.157
230.973
240.0398
250.623
260.0721
270.224
280.849
290.223
30.618
300.12
310.644
320.968
330.142
340.772
350.502
360.0794
370.248
380.132
390.604
40.593
400.00154
410.669
420.624
430.666
440.673
450.21
460.391
470.149
480.042
490.955
50.577
500.506
510.808
520.431
530.587
540.893
550.523
560.364
570.369
580.784
590.0539
60.231
600.228
610.489
620.899
630.279
640.166
650.326
660.206
670.965
680.911
690.337
70.203
700.0684
710.1
720.951
730.0402
740.041
750.206
760.719
770.0293
780.0594
790.467
80.141
800.729
810.965
820.774
830.993
840.732
850.899
860.919
870.00712
880.774
890.0607
90.642
900.00702
910.694
920.81
930.831
940.835
950.00644
960.654
970.712
980.205
990.0543



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: CNhs12054


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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