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FF:11292-117A5: 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 16:39, 29 March 2012


Name:Tracheal 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
tissuetrachea
dev stage50 years old adult
sexfemale
age50
cell typetracheal epithelial cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1875
catalog numberCA504-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-penis0.16
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-lymphoma0.0861
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: CNhs11092

Jaspar motifP-value
MA0002.20.544
MA0003.10.535
MA0004.10.476
MA0006.10.216
MA0007.10.321
MA0009.10.1
MA0014.10.346
MA0017.10.17
MA0018.20.0401
MA0019.10.399
MA0024.10.934
MA0025.10.483
MA0027.10.319
MA0028.10.00752
MA0029.10.711
MA0030.10.571
MA0031.10.124
MA0035.20.501
MA0038.10.942
MA0039.20.00144
MA0040.10.318
MA0041.10.617
MA0042.10.507
MA0043.10.971
MA0046.10.288
MA0047.20.171
MA0048.10.419
MA0050.15.52629e-11
MA0051.15.67232e-5
MA0052.10.224
MA0055.11.38501e-4
MA0057.10.0552
MA0058.10.198
MA0059.10.377
MA0060.10.498
MA0061.10.536
MA0062.20.0278
MA0065.20.0217
MA0066.10.232
MA0067.10.126
MA0068.10.0115
MA0069.10.782
MA0070.10.915
MA0071.10.246
MA0072.10.873
MA0073.10.737
MA0074.10.337
MA0076.10.143
MA0077.10.691
MA0078.10.812
MA0079.20.772
MA0080.20.0449
MA0081.10.362
MA0083.10.114
MA0084.10.329
MA0087.10.838
MA0088.10.214
MA0090.10.00152
MA0091.10.166
MA0092.10.56
MA0093.10.361
MA0099.23.13058e-14
MA0100.10.222
MA0101.10.774
MA0102.20.704
MA0103.11.50996e-7
MA0104.20.654
MA0105.10.457
MA0106.19.16578e-12
MA0107.10.824
MA0108.20.96
MA0111.10.758
MA0112.20.0744
MA0113.10.447
MA0114.10.0537
MA0115.10.58
MA0116.10.0657
MA0117.10.778
MA0119.10.159
MA0122.10.95
MA0124.10.342
MA0125.10.057
MA0131.10.911
MA0135.10.993
MA0136.10.17
MA0137.20.0483
MA0138.20.928
MA0139.10.506
MA0140.10.667
MA0141.10.773
MA0142.10.198
MA0143.10.98
MA0144.10.877
MA0145.10.0343
MA0146.10.167
MA0147.10.41
MA0148.10.0299
MA0149.10.0285
MA0150.10.133
MA0152.10.561
MA0153.10.371
MA0154.10.21
MA0155.10.904
MA0156.10.146
MA0157.10.098
MA0159.10.269
MA0160.10.912
MA0162.10.11
MA0163.10.254
MA0164.10.831
MA0258.10.799
MA0259.10.734



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: CNhs11092

Novel motifP-value
10.3
100.788
1000.343
1010.0168
1020.255
1030.204
1040.265
1050.0248
1060.0896
1070.032
1080.666
1090.0015
110.108
1100.0577
1110.144
1120.711
1130.393
1140.251
1150.798
1160.863
1170.191
1180.889
1190.148
120.451
1200.0287
1210.889
1220.0261
1230.893
1240.477
1250.414
1260.656
1270.147
1280.692
1290.192
130.0127
1300.751
1310.555
1320.414
1337.85303e-4
1340.343
1350.989
1360.164
1370.189
1380.887
1390.965
140.88
1400.456
1410.426
1420.262
1430.853
1440.074
1450.116
1460.00515
1470.0781
1480.366
1490.886
150.895
1500.263
1510.435
1520.0459
1530.32
1540.793
1550.872
1560.364
1570.515
1580.167
1590.402
160.0798
1600.169
1610.655
1620.216
1630.909
1640.364
1650.497
1660.304
1670.452
1680.549
1690.0563
170.136
180.218
190.863
20.368
200.479
210.792
220.383
230.438
240.0318
250.719
260.228
270.643
280.586
290.269
30.415
300.133
310.934
320.145
330.0561
340.9
350.379
360.306
370.32
380.272
390.298
40.423
400.00949
410.455
420.395
430.526
440.761
450.225
460.59
470.155
480.032
490.856
50.724
500.366
510.96
520.581
530.524
540.791
550.792
560.337
570.226
580.762
590.246
60.35
600.281
610.529
620.962
630.107
640.242
650.476
660.168
670.778
680.454
690.696
70.182
700.0257
710.107
720.88
730.0295
740.0179
750.0821
760.817
770.0294
780.00998
790.125
80.238
800.94
810.497
820.978
830.406
840.741
850.958
860.871
870.0333
880.5
890.117
90.995
900.958
910.677
920.955
930.959
940.729
950.0607
960.82
970.811
980.762
990.0404



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: CNhs11092


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)
0000068 (duct epithelial cell)
0000069 (branched duct epithelial cell)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000307 (tracheal epithelial cell)
0000377 (tracheoblast)
0000548 (animal cell)
0002076 (endo-epithelial cell)
0002202 (epithelial cell of tracheobronchial tree)
0002321 (embryonic 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)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001005 (respiratory airway)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001558 (lower respiratory tract)
0002050 (embryonic structure)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003126 (trachea)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
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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