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FF:11399-118D4: 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 17:06, 29 March 2012


Name:Ciliary Epithelial Cells, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueeye
dev stagefetus
sexunknown
agefetal
cell typeciliated epithelial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3062
catalog numberSC6585
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-penis0.0858
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-lymphoma0.213
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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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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: CNhs12009

Jaspar motifP-value
MA0002.20.011
MA0003.10.0495
MA0004.10.1
MA0006.10.465
MA0007.10.267
MA0009.10.33
MA0014.10.277
MA0017.10.0258
MA0018.20.399
MA0019.10.734
MA0024.10.0446
MA0025.10.778
MA0027.10.744
MA0028.10.774
MA0029.10.532
MA0030.10.00342
MA0031.10.00114
MA0035.20.0502
MA0038.10.0262
MA0039.20.564
MA0040.10.205
MA0041.10.274
MA0042.10.163
MA0043.10.31
MA0046.10.514
MA0047.27.68234e-5
MA0048.10.252
MA0050.10.00112
MA0051.10.00816
MA0052.10.0518
MA0055.10.851
MA0057.10.466
MA0058.10.0443
MA0059.10.0519
MA0060.11.26543e-5
MA0061.10.00133
MA0062.20.226
MA0065.20.00402
MA0066.10.233
MA0067.10.0378
MA0068.10.0073
MA0069.10.739
MA0070.10.965
MA0071.10.133
MA0072.10.486
MA0073.10.782
MA0074.10.293
MA0076.10.804
MA0077.10.0802
MA0078.10.37
MA0079.20.764
MA0080.26.08542e-12
MA0081.10.0975
MA0083.10.00278
MA0084.10.474
MA0087.10.394
MA0088.10.0309
MA0090.10.00685
MA0091.10.0496
MA0092.10.161
MA0093.10.127
MA0099.22.95288e-5
MA0100.10.867
MA0101.10.0407
MA0102.20.00199
MA0103.10.111
MA0104.20.0268
MA0105.12.11274e-6
MA0106.10.306
MA0107.10.00369
MA0108.20.00522
MA0111.10.494
MA0112.22.01095e-5
MA0113.10.0325
MA0114.10.0377
MA0115.10.288
MA0116.14.42022e-5
MA0117.10.699
MA0119.10.312
MA0122.10.999
MA0124.10.975
MA0125.10.152
MA0131.10.743
MA0135.10.215
MA0136.12.73582e-13
MA0137.20.37
MA0138.20.2
MA0139.10.211
MA0140.10.0315
MA0141.10.0265
MA0142.10.103
MA0143.10.282
MA0144.10.256
MA0145.10.325
MA0146.10.147
MA0147.10.0485
MA0148.15.69592e-4
MA0149.10.0407
MA0150.12.1166e-4
MA0152.10.395
MA0153.10.828
MA0154.10.00209
MA0155.10.706
MA0156.11.75609e-5
MA0157.10.0231
MA0159.10.0145
MA0160.10.0131
MA0162.10.236
MA0163.16.6888e-7
MA0164.10.834
MA0258.10.00299
MA0259.10.225



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: CNhs12009

Novel motifP-value
10.0536
100.1
1000.978
1010.7
1020.501
1030.193
1040.742
1050.168
1060.0872
1070.993
1080.511
1090.0605
110.0497
1100.343
1110.00424
1120.0156
1130.672
1140.0419
1150.343
1160.793
1170.173
1180.228
1190.353
120.431
1200.423
1210.814
1220.521
1230.0855
1240.3
1250.642
1260.146
1270.195
1280.245
1290.167
130.346
1300.305
1310.966
1320.818
1330.574
1340.805
1350.00827
1360.396
1370.181
1380.166
1390.128
140.793
1400.376
1410.148
1420.435
1430.26
1440.827
1450.509
1460.509
1470.777
1480.0075
1490.0588
150.0808
1500.701
1510.195
1520.364
1530.216
1540.793
1550.021
1560.0374
1570.638
1580.0315
1590.793
160.327
1600.143
1610.491
1620.241
1630.389
1640.252
1650.243
1660.211
1670.682
1680.459
1690.00985
170.132
180.063
190.296
20.564
200.773
210.972
220.215
230.137
240.336
250.271
260.223
270.345
280.947
290.0933
30.17
300.936
310.576
320.554
330.25
340.639
350.232
360.0137
370.0931
380.146
390.652
40.747
400.0518
410.0256
420.336
430.0849
440.698
450.545
460.0621
470.148
480.182
490.0514
50.146
500.692
510.5
520.565
530.43
540.418
550.547
560.468
570.404
580.121
590.135
60.911
600.0816
610.232
620.0628
630.15
640.183
650.157
660.911
670.714
680.158
690.66
70.231
700.0128
710.0732
720.111
730.137
740.31
750.0319
760.187
770.178
780.382
790.815
80.314
800.163
810.343
820.0379
830.573
840.313
850.0366
860.179
870.46
880.884
890.229
90.352
900.236
910.897
920.177
930.0267
940.0712
950.0781
960.0911
970.866
980.0352
990.267



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: CNhs12009


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)
0000064 (ciliated cell)
0000066 (epithelial cell)
0000067 (ciliated epithelial cell)
0000075 (columnar/cuboidal epithelial cell)
0000133 (neurectodermal cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000710 (neurecto-epithelial cell)
0002077 (ecto-epithelial cell)
0002304 (non-pigmented ciliary epithelial cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0005012 (multi-ciliated epithelial cell)

UBERON: Anatomy
0000019 (camera-type eye)
0000020 (sense organ)
0000033 (head)
0000047 (simple eye)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000119 (cell layer)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000488 (atypical epithelium)
0000970 (eye)
0001009 (circulatory system)
0001032 (sensory system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001768 (uvea)
0001775 (ciliary body)
0001778 (ciliary epithelium)
0001801 (anterior segment of eyeball)
0002049 (vasculature)
0002104 (visual system)
0002200 (vasculature of head)
0002203 (vasculature of eye)
0004456 (entire sense organ system)
0004535 (cardiovascular system)
0006876 (vasculature of organ)
0007625 (pigment epithelium of eye)
0007798 (vascular system)

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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