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FF:11242-116D9: 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 16:36, 29 March 2012


Name:Ciliary 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
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 number579
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-penis-0.0901
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-lymphoma0.434
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs10871

Jaspar motifP-value
MA0002.20.00674
MA0003.10.0526
MA0004.10.159
MA0006.10.798
MA0007.10.276
MA0009.10.281
MA0014.10.493
MA0017.10.0163
MA0018.20.969
MA0019.10.857
MA0024.10.00137
MA0025.10.867
MA0027.10.353
MA0028.10.176
MA0029.10.224
MA0030.10.276
MA0031.10.0647
MA0035.20.0276
MA0038.14.7716e-5
MA0039.20.701
MA0040.10.904
MA0041.10.372
MA0042.10.295
MA0043.10.738
MA0046.10.812
MA0047.21.01099e-4
MA0048.10.458
MA0050.10.102
MA0051.10.499
MA0052.10.0928
MA0055.10.879
MA0057.10.306
MA0058.10.108
MA0059.10.0345
MA0060.13.03004e-11
MA0061.10.0156
MA0062.20.964
MA0065.20.00122
MA0066.10.074
MA0067.10.296
MA0068.11.29565e-4
MA0069.10.793
MA0070.10.106
MA0071.10.136
MA0072.10.989
MA0073.10.716
MA0074.10.195
MA0076.10.161
MA0077.10.0538
MA0078.10.949
MA0079.20.665
MA0080.24.21146e-12
MA0081.10.171
MA0083.10.0958
MA0084.10.689
MA0087.10.829
MA0088.10.13
MA0090.10.0791
MA0091.10.046
MA0092.10.209
MA0093.10.198
MA0099.24.97764e-4
MA0100.10.516
MA0101.10.241
MA0102.20.0692
MA0103.10.034
MA0104.20.0924
MA0105.14.62124e-4
MA0106.10.106
MA0107.10.0734
MA0108.20.286
MA0111.10.665
MA0112.22.47948e-6
MA0113.10.0462
MA0114.10.11
MA0115.10.203
MA0116.13.12088e-4
MA0117.10.518
MA0119.10.283
MA0122.10.703
MA0124.10.338
MA0125.10.0103
MA0131.10.646
MA0135.10.198
MA0136.12.17106e-10
MA0137.20.464
MA0138.20.0485
MA0139.10.375
MA0140.10.0391
MA0141.10.0248
MA0142.10.0934
MA0143.10.0741
MA0144.10.446
MA0145.10.468
MA0146.10.0842
MA0147.10.076
MA0148.10.00204
MA0149.10.0296
MA0150.17.1032e-4
MA0152.10.0948
MA0153.10.625
MA0154.10.00307
MA0155.10.336
MA0156.10.00154
MA0157.10.126
MA0159.10.0205
MA0160.10.0268
MA0162.10.157
MA0163.15.72723e-7
MA0164.10.47
MA0258.13.89613e-4
MA0259.10.395



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: CNhs10871

Novel motifP-value
10.0707
100.127
1000.901
1010.552
1020.507
1030.174
1040.672
1050.934
1060.00927
1070.623
1080.331
1090.0749
110.0454
1100.379
1110.00319
1120.018
1130.375
1140.0212
1150.614
1160.723
1170.167
1180.243
1190.126
120.555
1200.58
1210.995
1220.845
1230.0537
1240.625
1250.231
1260.242
1270.0657
1280.111
1290.233
130.456
1300.0423
1310.601
1320.744
1330.562
1340.936
1350.0292
1360.643
1370.29
1380.101
1390.00799
140.872
1400.108
1410.127
1420.756
1430.0194
1440.894
1450.802
1460.821
1470.918
1480.0136
1490.0819
150.0869
1500.381
1510.214
1520.0438
1530.237
1540.897
1550.0113
1560.343
1570.258
1580.075
1590.546
160.213
1600.0798
1610.594
1620.567
1630.659
1640.0847
1650.648
1660.197
1670.336
1680.654
1690.00463
170.0645
180.0329
190.244
20.467
200.937
210.42
220.243
230.107
240.75
250.434
260.179
270.316
280.941
290.13
30.113
300.853
310.435
320.166
330.48
340.532
350.279
360.0386
370.089
380.165
390.839
40.653
400.085
410.0847
420.335
430.1
440.16
450.552
460.0505
470.176
480.189
490.0637
50.148
500.766
510.404
520.525
530.657
540.345
550.605
560.506
570.434
580.181
590.076
60.865
600.0751
610.217
620.0675
630.137
640.181
650.0721
660.467
670.319
680.881
690.247
70.397
700.00528
710.116
720.282
730.0456
740.487
750.0349
760.166
770.136
780.546
790.0552
80.16
800.74
810.32
820.0246
830.576
840.173
850.0121
860.121
870.513
880.786
890.0779
90.424
900.497
910.55
920.0994
930.0382
940.0475
950.0472
960.12
970.97
980.0793
990.579



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: CNhs10871


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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