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FF:10054-101G9: 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 16:51, 29 March 2012


Name:eye, fetal, 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 stage36 weeks fetus
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB210179
catalog numberCat:RtHFN: Whole Eye
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-Neural0.0885
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-penis0.00394
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-0.318
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0.0885
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs11762

Jaspar motifP-value
MA0002.25.5093e-4
MA0003.10.693
MA0004.10.0375
MA0006.10.746
MA0007.10.221
MA0009.10.0831
MA0014.10.263
MA0017.10.0637
MA0018.20.779
MA0019.10.169
MA0024.10.192
MA0025.10.945
MA0027.10.797
MA0028.12.75725e-5
MA0029.10.179
MA0030.10.213
MA0031.10.97
MA0035.20.271
MA0038.10.283
MA0039.20.202
MA0040.10.729
MA0041.10.127
MA0042.10.303
MA0043.10.0594
MA0046.10.0517
MA0047.20.405
MA0048.10.0798
MA0050.15.00189e-5
MA0051.10.00197
MA0052.11.68873e-6
MA0055.13.45726e-4
MA0057.10.817
MA0058.10.0317
MA0059.10.0115
MA0060.10.498
MA0061.11.77866e-4
MA0062.21.96295e-10
MA0065.20.0194
MA0066.10.186
MA0067.10.463
MA0068.10.0047
MA0069.10.787
MA0070.10.959
MA0071.10.579
MA0072.10.558
MA0073.10.386
MA0074.10.876
MA0076.13.79255e-6
MA0077.10.953
MA0078.10.454
MA0079.20.869
MA0080.28.92928e-9
MA0081.10.00557
MA0083.10.692
MA0084.10.414
MA0087.10.235
MA0088.10.0118
MA0090.10.917
MA0091.10.212
MA0092.10.789
MA0093.10.0434
MA0099.21.01185e-20
MA0100.10.0898
MA0101.12.93549e-5
MA0102.20.0857
MA0103.10.722
MA0104.20.0219
MA0105.12.37162e-6
MA0106.10.00793
MA0107.17.01144e-5
MA0108.22.20399e-21
MA0111.10.693
MA0112.20.0665
MA0113.10.868
MA0114.10.0131
MA0115.10.121
MA0116.10.0141
MA0117.10.408
MA0119.10.176
MA0122.10.461
MA0124.10.68
MA0125.10.117
MA0131.10.45
MA0135.10.0569
MA0136.11.4252e-13
MA0137.20.978
MA0138.20.00508
MA0139.10.197
MA0140.10.31
MA0141.10.0882
MA0142.10.064
MA0143.10.785
MA0144.10.529
MA0145.10.716
MA0146.10.00747
MA0147.10.00623
MA0148.10.414
MA0149.10.00837
MA0150.16.66294e-7
MA0152.10.381
MA0153.10.997
MA0154.10.0783
MA0155.10.515
MA0156.11.14165e-12
MA0157.10.287
MA0159.10.103
MA0160.10.0443
MA0162.10.47
MA0163.14.64551e-7
MA0164.10.287
MA0258.10.25
MA0259.10.326



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: CNhs11762

Novel motifP-value
10.0354
100.0134
1000.368
1010.916
1020.837
1030.173
1040.591
1050.371
1060.441
1070.829
1080.815
1090.0126
110.036
1100.0913
1110.00667
1120.846
1130.0335
1140.103
1150.135
1160.816
1170.00254
1180.0315
1190.376
120.861
1200.448
1210.763
1220.919
1230.0107
1240.444
1250.69
1260.112
1270.629
1280.83
1290.324
130.00372
1300.912
1310.227
1320.194
1330.0493
1340.476
1350.819
1360.046
1370.494
1380.334
1390.596
140.748
1400.4
1410.145
1420.83
1430.00503
1440.708
1450.466
1460.336
1470.146
1480.213
1490.768
150.0116
1500.304
1510.702
1520.122
1530.795
1540.768
1550.119
1560.792
1570.274
1580.215
1590.961
160.661
1600.523
1610.153
1620.349
1630.759
1640.00696
1650.613
1660.245
1670.0351
1680.937
1690.00934
170.268
180.138
190.878
20.258
200.0327
210.183
220.446
230.731
240.185
250.406
260.00212
270.769
280.569
290.00289
30.0252
300.0559
310.759
320.0376
330.0408
340.466
350.672
360.114
370.0341
380.478
390.902
40.848
400.135
410.117
420.0815
430.175
440.934
450.708
460.148
470.0361
480.081
490.133
50.355
500.608
510.518
520.682
530.778
540.668
550.138
560.705
570.14
580.434
590.859
60.859
600.43
610.0104
620.378
630.246
640.472
650.742
660.0282
670.575
680.24
690.877
70.104
700.11
710.00604
720.308
730.0171
740.26
750.00242
760.039
770.773
780.0966
790.781
80.0586
800.736
810.498
820.918
830.927
840.423
850.676
860.158
870.00166
880.5
890.845
90.823
900.0801
910.787
920.803
930.921
940.0346
950.0129
960.43
970.793
980.256
990.371



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: CNhs11762


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

UBERON: Anatomy
0000020 (sense organ)
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000970 (eye)
0001032 (sensory system)
0001062 (anatomical entity)
0002104 (visual system)
0004456 (entire sense organ 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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