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FF:11693-123A1: 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 17:12, 29 March 2012


Name:Trabecular Meshwork 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 stageNA
sexNA
ageNA
cell typetrabecular meshwork cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC6595
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-0.0578
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-lymphoma0.0901
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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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: CNhs12124

Jaspar motifP-value
MA0002.20.288
MA0003.10.276
MA0004.10.709
MA0006.10.302
MA0007.10.0912
MA0009.10.167
MA0014.10.937
MA0017.10.854
MA0018.20.51
MA0019.10.902
MA0024.10.0357
MA0025.10.559
MA0027.10.26
MA0028.10.619
MA0029.10.593
MA0030.10.739
MA0031.10.107
MA0035.20.686
MA0038.16.37419e-4
MA0039.20.144
MA0040.10.444
MA0041.10.232
MA0042.10.477
MA0043.10.636
MA0046.10.0242
MA0047.20.62
MA0048.10.0959
MA0050.11.20175e-4
MA0051.10.00457
MA0052.10.395
MA0055.10.00151
MA0057.10.691
MA0058.10.996
MA0059.10.621
MA0060.15.15064e-8
MA0061.10.144
MA0062.20.294
MA0065.20.891
MA0066.10.432
MA0067.10.0619
MA0068.10.293
MA0069.10.76
MA0070.10.00299
MA0071.10.505
MA0072.10.978
MA0073.10.824
MA0074.10.464
MA0076.10.998
MA0077.10.201
MA0078.10.973
MA0079.20.282
MA0080.23.37535e-6
MA0081.10.185
MA0083.10.0466
MA0084.10.115
MA0087.10.494
MA0088.10.609
MA0090.10.265
MA0091.10.254
MA0092.10.756
MA0093.10.786
MA0099.20.74
MA0100.10.556
MA0101.10.346
MA0102.20.16
MA0103.10.263
MA0104.20.284
MA0105.10.154
MA0106.10.642
MA0107.10.258
MA0108.22.90343e-6
MA0111.10.0644
MA0112.20.744
MA0113.10.126
MA0114.10.792
MA0115.10.541
MA0116.10.435
MA0117.10.117
MA0119.10.888
MA0122.10.349
MA0124.10.932
MA0125.10.794
MA0131.10.708
MA0135.10.014
MA0136.14.16934e-5
MA0137.20.251
MA0138.20.525
MA0139.10.691
MA0140.10.917
MA0141.10.5
MA0142.10.547
MA0143.10.0942
MA0144.10.342
MA0145.10.589
MA0146.10.00792
MA0147.10.297
MA0148.10.363
MA0149.10.176
MA0150.10.0294
MA0152.10.885
MA0153.10.134
MA0154.10.711
MA0155.10.133
MA0156.10.0133
MA0157.10.0786
MA0159.10.0685
MA0160.10.889
MA0162.10.253
MA0163.10.947
MA0164.10.821
MA0258.10.944
MA0259.10.508



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: CNhs12124

Novel motifP-value
10.0889
100.0416
1000.436
1010.0895
1020.895
1030.103
1040.201
1050.243
1060.881
1070.257
1080.372
1090.579
110.74
1100.397
1110.026
1120.393
1130.214
1140.0393
1150.294
1160.526
1170.976
1180.639
1190.224
120.775
1200.354
1210.806
1220.589
1232.97115e-4
1240.148
1250.178
1260.872
1270.405
1280.668
1290.549
130.591
1300.00993
1310.75
1320.228
1330.142
1340.832
1350.145
1360.203
1370.00981
1380.0974
1390.0126
140.623
1400.294
1410.272
1420.193
1430.466
1440.939
1450.929
1460.283
1470.997
1480.0544
1490.965
150.0925
1500.275
1510.95
1520.0693
1530.315
1540.0772
1550.298
1560.845
1570.617
1580.0329
1590.988
160.999
1600.332
1610.764
1620.0933
1630.696
1640.708
1650.0158
1660.815
1670.0391
1680.756
1690.295
170.99
180.862
190.361
20.462
200.994
210.679
220.216
230.388
240.746
250.0643
260.427
270.917
280.106
290.602
30.346
300.163
310.627
320.0034
330.654
340.324
350.268
360.197
370.932
380.744
390.916
40.969
400.287
410.146
420.263
430.48
440.425
450.238
460.673
470.803
480.641
490.223
50.095
500.366
510.989
520.629
530.221
540.865
550.449
560.788
570.262
580.0254
590.147
60.519
600.396
610.895
620.021
630.999
640.665
650.567
660.275
670.353
680.0124
690.316
70.172
700.563
710.0948
720.364
730.0151
740.385
750.768
760.318
770.534
780.35
790.782
80.982
800.589
810.375
820.209
830.44
840.866
850.599
860.823
870.0919
880.361
890.927
90.379
900.00369
910.368
920.203
930.275
940.251
950.196
960.337
970.963
980.67
990.00332



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: CNhs12124


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)
0000115 (endothelial cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002078 (meso-epithelial cell)
0002321 (embryonic cell)
0002367 (trabecular meshwork cell)
0002371 (somatic 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)
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)
0000970 (eye)
0001009 (circulatory system)
0001032 (sensory system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001768 (uvea)
0001801 (anterior segment of eyeball)
0002049 (vasculature)
0002104 (visual system)
0002200 (vasculature of head)
0002203 (vasculature of eye)
0003956 (aqueous drainage system)
0004456 (entire sense organ system)
0004535 (cardiovascular system)
0005969 (reticulum trabeculare)
0006876 (vasculature of organ)
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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