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FF:11334-117F2: 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 17:04, 29 March 2012


Name:Small Airway 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
tissuelung
dev stage58 years old adult
sexmale
age58
cell typepneumocyte
cell lineNA
companyLonza
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-penis0.0666
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-0.233
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: CNhs11975

Jaspar motifP-value
MA0002.20.0143
MA0003.10.75
MA0004.10.185
MA0006.10.0134
MA0007.10.409
MA0009.10.184
MA0014.10.499
MA0017.10.531
MA0018.20.0312
MA0019.10.913
MA0024.13.61734e-5
MA0025.10.601
MA0027.10.555
MA0028.10.0747
MA0029.10.0524
MA0030.10.855
MA0031.10.636
MA0035.20.512
MA0038.14.50989e-4
MA0039.20.0596
MA0040.10.377
MA0041.10.535
MA0042.10.232
MA0043.10.456
MA0046.10.888
MA0047.20.204
MA0048.10.594
MA0050.14.50827e-9
MA0051.11.64954e-6
MA0052.10.00152
MA0055.10.0465
MA0057.10.155
MA0058.10.0214
MA0059.10.661
MA0060.12.43706e-6
MA0061.10.0322
MA0062.20.67
MA0065.20.746
MA0066.10.774
MA0067.10.057
MA0068.10.093
MA0069.10.214
MA0070.10.242
MA0071.10.199
MA0072.10.36
MA0073.10.843
MA0074.10.771
MA0076.10.473
MA0077.10.377
MA0078.10.907
MA0079.20.0921
MA0080.22.89197e-5
MA0081.10.0146
MA0083.10.0895
MA0084.10.182
MA0087.10.76
MA0088.10.129
MA0090.10.00226
MA0091.10.21
MA0092.10.35
MA0093.10.113
MA0099.20.0651
MA0100.10.0252
MA0101.10.128
MA0102.20.941
MA0103.11.10443e-7
MA0104.20.0481
MA0105.10.0027
MA0106.11.281e-10
MA0107.10.0878
MA0108.20.709
MA0111.10.753
MA0112.20.334
MA0113.10.971
MA0114.10.286
MA0115.10.975
MA0116.10.0339
MA0117.10.193
MA0119.10.824
MA0122.10.312
MA0124.10.28
MA0125.10.143
MA0131.10.98
MA0135.10.725
MA0136.10.00267
MA0137.20.00348
MA0138.20.995
MA0139.10.478
MA0140.10.415
MA0141.10.743
MA0142.10.369
MA0143.10.917
MA0144.10.444
MA0145.10.0402
MA0146.10.368
MA0147.10.0802
MA0148.10.144
MA0149.10.178
MA0150.10.172
MA0152.10.321
MA0153.10.43
MA0154.10.155
MA0155.10.433
MA0156.10.126
MA0157.10.185
MA0159.10.766
MA0160.10.599
MA0162.10.468
MA0163.10.00723
MA0164.10.992
MA0258.10.186
MA0259.10.999



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: CNhs11975

Novel motifP-value
10.418
100.0818
1000.599
1010.0213
1020.324
1030.301
1040.858
1050.77
1060.0412
1070.0947
1080.0786
1090.0966
110.906
1100.961
1110.441
1120.724
1130.999
1140.761
1150.305
1160.634
1170.973
1180.607
1190.774
120.596
1200.077
1210.685
1220.537
1230.671
1240.0105
1250.741
1260.862
1270.584
1280.817
1290.59
130.721
1300.172
1310.896
1320.273
1335.19342e-4
1340.092
1350.72
1368.81196e-4
1370.003
1380.732
1390.665
140.757
1400.248
1410.442
1420.379
1430.166
1440.0797
1450.549
1460.191
1470.101
1480.0598
1490.822
150.214
1500.222
1510.284
1528.28033e-4
1530.505
1540.973
1550.654
1560.897
1570.253
1580.0714
1590.772
160.0665
1600.1
1610.524
1620.692
1630.567
1640.428
1650.891
1660.688
1670.366
1680.614
1690.465
170.46
180.293
190.459
20.369
200.552
210.897
220.948
230.425
240.201
250.31
260.84
270.786
280.86
290.721
30.541
300.174
310.984
320.788
330.489
340.523
350.0152
360.0433
370.633
380.944
390.505
40.689
400.885
410.153
420.459
430.324
440.64
450.211
460.773
470.784
480.793
490.0104
50.364
500.708
510.621
520.148
530.0403
540.888
550.609
560.795
570.775
580.349
590.421
60.0696
600.286
610.972
620.185
630.595
640.721
650.964
660.715
670.66
680.439
690.678
70.651
700.04
710.132
720.634
736.23061e-4
740.00891
750.807
760.313
770.409
780.108
790.246
80.927
800.121
810.114
820.232
830.264
840.445
850.538
860.868
870.0108
880.661
890.297
90.226
900.309
910.447
920.457
930.373
940.296
950.109
960.248
970.713
980.194
990.107



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: CNhs11975


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)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002076 (endo-epithelial cell)
0002321 (embryonic cell)
0002368 (respiratory epithelial cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000065 (respiratory tract)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001004 (respiratory system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0005423 (developing anatomical structure)

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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