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FF:11369-118A1: 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 17:05, 29 March 2012


Name:Tracheal Epithelial Cells, donor2
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 stage45 years old adult
sexmale
age45
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 number1217
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-penis-0.0899
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-0.0868
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11993

Jaspar motifP-value
MA0002.20.314
MA0003.10.276
MA0004.10.784
MA0006.10.13
MA0007.10.114
MA0009.10.0913
MA0014.10.613
MA0017.10.137
MA0018.20.0609
MA0019.10.249
MA0024.10.293
MA0025.10.393
MA0027.10.483
MA0028.10.725
MA0029.10.708
MA0030.10.903
MA0031.10.115
MA0035.20.343
MA0038.10.445
MA0039.20.00772
MA0040.10.581
MA0041.10.26
MA0042.10.856
MA0043.10.172
MA0046.10.877
MA0047.20.725
MA0048.10.704
MA0050.12.98038e-7
MA0051.10.00137
MA0052.10.66
MA0055.10.0401
MA0057.10.0716
MA0058.10.56
MA0059.10.441
MA0060.10.275
MA0061.10.627
MA0062.20.67
MA0065.20.00522
MA0066.10.0288
MA0067.10.279
MA0068.10.0237
MA0069.10.651
MA0070.10.91
MA0071.10.826
MA0072.10.488
MA0073.10.65
MA0074.10.299
MA0076.10.249
MA0077.10.659
MA0078.10.794
MA0079.20.361
MA0080.20.299
MA0081.10.881
MA0083.10.032
MA0084.10.342
MA0087.10.693
MA0088.10.443
MA0090.10.00931
MA0091.10.913
MA0092.10.349
MA0093.10.643
MA0099.29.80963e-18
MA0100.10.036
MA0101.10.997
MA0102.20.13
MA0103.16.92503e-5
MA0104.20.857
MA0105.10.754
MA0106.12.53547e-6
MA0107.10.801
MA0108.23.63079e-15
MA0111.10.583
MA0112.20.016
MA0113.10.675
MA0114.10.0542
MA0115.10.617
MA0116.10.202
MA0117.10.589
MA0119.10.147
MA0122.10.813
MA0124.10.433
MA0125.10.208
MA0131.10.305
MA0135.10.0322
MA0136.10.131
MA0137.20.148
MA0138.20.152
MA0139.10.8
MA0140.10.833
MA0141.10.351
MA0142.10.0143
MA0143.10.473
MA0144.10.904
MA0145.10.0248
MA0146.10.038
MA0147.10.912
MA0148.10.64
MA0149.10.173
MA0150.10.0614
MA0152.10.0849
MA0153.10.188
MA0154.10.237
MA0155.10.238
MA0156.10.514
MA0157.10.288
MA0159.10.29
MA0160.10.22
MA0162.10.117
MA0163.10.43
MA0164.10.929
MA0258.10.038
MA0259.10.768



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: CNhs11993

Novel motifP-value
10.638
100.55
1000.382
1010.00351
1020.24
1030.274
1040.396
1050.0712
1060.0189
1070.0152
1080.527
1090.00661
110.144
1100.109
1110.789
1120.299
1130.424
1140.662
1150.15
1160.183
1170.433
1180.877
1190.185
120.247
1200.37
1210.127
1220.0167
1230.411
1240.421
1250.87
1260.82
1270.0241
1280.197
1290.439
130.0488
1300.327
1310.369
1320.711
1330.0227
1340.209
1350.267
1360.176
1370.159
1380.672
1390.862
140.786
1400.698
1410.71
1420.0256
1430.618
1440.249
1450.189
1460.00198
1470.273
1480.883
1490.851
150.942
1500.143
1510.355
1520.0368
1530.896
1540.443
1550.546
1560.746
1570.998
1580.244
1590.76
160.0706
1600.186
1610.396
1620.0859
1630.845
1640.75
1650.526
1660.218
1670.269
1680.545
1690.0686
170.108
180.659
190.46
20.113
200.671
210.673
220.147
230.333
240.0413
250.971
260.0696
270.205
280.924
290.735
30.734
300.125
310.674
320.622
330.236
340.326
350.49
360.596
370.22
380.372
390.198
40.605
400.0134
410.879
420.983
430.497
440.924
450.0774
460.387
470.33
480.113
490.909
50.389
500.422
510.622
520.296
530.517
540.773
550.781
560.419
570.691
580.879
590.0564
60.203
600.259
610.928
620.931
630.184
640.367
650.158
660.557
670.639
680.885
690.117
70.388
700.0472
710.353
720.806
730.023
740.0907
750.449
760.814
770.018
780.144
790.99
80.14
800.898
810.745
820.78
830.859
840.72
850.371
860.919
870.0138
880.519
890.198
90.437
900.0036
910.725
920.769
930.72
940.688
950.141
960.761
970.741
980.287
990.0305



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: CNhs11993


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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