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FF:10277-104E7: 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 17:32, 29 March 2012


Name:optic nerve, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueoptic nerve
dev stageNA
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationAlessandro Bonetti
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1-On
catalog numberNA
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-penis0.63
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs13449

Jaspar motifP-value
MA0002.20.124
MA0003.10.253
MA0004.10.159
MA0006.10.607
MA0007.10.636
MA0009.10.213
MA0014.10.382
MA0017.10.0115
MA0018.20.146
MA0019.10.918
MA0024.10.784
MA0025.10.654
MA0027.10.691
MA0028.10.00282
MA0029.10.297
MA0030.10.0961
MA0031.10.0926
MA0035.20.193
MA0038.10.769
MA0039.20.0351
MA0040.10.96
MA0041.10.703
MA0042.10.905
MA0043.10.806
MA0046.10.0953
MA0047.20.628
MA0048.10.0576
MA0050.10.00298
MA0051.10.0876
MA0052.10.202
MA0055.10.0019
MA0057.10.641
MA0058.10.229
MA0059.10.0507
MA0060.10.321
MA0061.16.3616e-4
MA0062.21.83862e-6
MA0065.20.0306
MA0066.10.0135
MA0067.10.712
MA0068.10.359
MA0069.10.864
MA0070.10.95
MA0071.10.0747
MA0072.10.82
MA0073.10.318
MA0074.10.395
MA0076.10.00168
MA0077.14.65675e-4
MA0078.10.06
MA0079.20.665
MA0080.28.91792e-7
MA0081.10.00652
MA0083.10.0781
MA0084.10.044
MA0087.10.0997
MA0088.10.25
MA0090.10.392
MA0091.10.535
MA0092.10.748
MA0093.10.17
MA0099.28.81409e-16
MA0100.10.277
MA0101.18.24592e-5
MA0102.20.18
MA0103.10.0426
MA0104.20.232
MA0105.11.0735e-4
MA0106.10.125
MA0107.16.84232e-5
MA0108.20.206
MA0111.10.838
MA0112.20.0033
MA0113.10.656
MA0114.10.0462
MA0115.10.973
MA0116.13.57985e-4
MA0117.10.524
MA0119.10.447
MA0122.10.499
MA0124.10.988
MA0125.10.234
MA0131.10.896
MA0135.10.432
MA0136.12.27782e-12
MA0137.20.625
MA0138.20.411
MA0139.10.399
MA0140.10.463
MA0141.10.00489
MA0142.10.893
MA0143.10.0915
MA0144.10.844
MA0145.10.742
MA0146.10.0504
MA0147.10.13
MA0148.10.916
MA0149.10.0424
MA0150.12.29449e-4
MA0152.10.77
MA0153.10.671
MA0154.10.04
MA0155.10.554
MA0156.14.12888e-9
MA0157.10.273
MA0159.10.0385
MA0160.10.0935
MA0162.10.314
MA0163.11.44545e-6
MA0164.10.59
MA0258.10.111
MA0259.10.716



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: CNhs13449

Novel motifP-value
10.308
100.134
1000.788
1010.634
1020.651
1030.0219
1040.0227
1050.0587
1060.108
1070.513
1080.574
1090.00263
110.0122
1100.0553
1110.695
1120.44
1130.0204
1140.49
1150.419
1160.235
1170.0146
1180.369
1190.845
120.374
1200.0328
1210.848
1220.907
1230.00103
1240.536
1250.913
1260.145
1270.195
1280.698
1290.942
130.00522
1300.0568
1310.0035
1320.437
1330.114
1340.444
1350.879
1360.0031
1370.294
1380.463
1390.73
140.93
1400.179
1410.881
1420.497
1430.0808
1440.305
1450.792
1460.926
1470.985
1480.882
1490.177
150.102
1500.0808
1510.942
1520.0906
1530.297
1540.141
1550.771
1560.493
1570.434
1580.351
1590.0765
160.0549
1600.347
1610.329
1620.526
1630.798
1640.015
1650.0999
1660.821
1670.229
1680.67
1690.109
170.178
180.113
190.445
20.737
200.185
210.161
220.237
230.793
240.0022
250.467
260.143
270.297
280.936
295.1869e-4
30.0842
300.597
310.766
320.0243
330.15
340.667
350.749
360.583
370.0315
380.615
390.465
40.635
400.196
410.605
420.421
430.287
440.00703
450.824
460.085
470.0787
480.055
490.49
50.455
500.629
510.607
520.976
530.14
540.908
550.831
560.936
570.815
580.286
590.0326
60.55
600.203
610.13
620.135
630.96
640.178
650.381
660.0837
670.676
680.206
690.435
70.135
700.713
710.00806
720.0678
730.0226
740.79
750.0104
760.685
770.1
780.0165
790.15
80.104
800.324
810.532
820.96
830.0247
840.49
850.351
860.21
870.00108
880.578
890.128
90.252
900.626
910.363
920.668
930.569
940.466
950.00285
960.274
970.88
980.426
990.761



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: CNhs13449


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
0000010 (peripheral nervous system)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000073 (regional part of nervous system)
0000122 (neuron projection bundle)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000941 (cranial nerve II)
0001016 (nervous system)
0001021 (nerve)
0001032 (sensory system)
0001062 (anatomical entity)
0001785 (cranial nerve)
0002050 (embryonic structure)
0002104 (visual system)
0002464 (nerve trunk)
0002532 (epiblast (generic))
0003714 (neural tissue)
0004121 (ectoderm-derived structure)
0004456 (entire sense organ system)
0004732 (segmental subdivision of nervous system)
0004904 (nerve connecting eye with brain)
0005162 (multi cell component structure)
0005423 (developing anatomical structure)
0007023 (adult organism)

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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