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FF:11463-119B5: 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 17:10, 29 March 2012


Name:Anulus Pulposus Cell, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespinal cord
dev stageNA
sexunknown
ageNA
cell typeanulus fibrosus cell of intervertebral disc
cell lineNA
companySciencell
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:5027
catalog numberSC4815
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-0.073
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-0.367
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: CNhs12064

Jaspar motifP-value
MA0002.20.0694
MA0003.10.266
MA0004.10.43
MA0006.10.236
MA0007.10.29
MA0009.10.59
MA0014.10.601
MA0017.10.945
MA0018.20.00175
MA0019.10.459
MA0024.16.396e-6
MA0025.10.0295
MA0027.10.611
MA0028.10.00479
MA0029.10.849
MA0030.10.871
MA0031.10.759
MA0035.20.127
MA0038.10.209
MA0039.20.287
MA0040.10.275
MA0041.10.231
MA0042.10.25
MA0043.10.00773
MA0046.10.477
MA0047.20.34
MA0048.10.77
MA0050.18.49586e-7
MA0051.10.00365
MA0052.10.946
MA0055.10.44
MA0057.10.775
MA0058.10.311
MA0059.10.152
MA0060.12.47137e-5
MA0061.10.218
MA0062.24.07897e-8
MA0065.20.944
MA0066.10.413
MA0067.10.0402
MA0068.10.167
MA0069.10.746
MA0070.10.848
MA0071.10.923
MA0072.10.526
MA0073.10.926
MA0074.10.304
MA0076.10.00103
MA0077.10.227
MA0078.10.653
MA0079.20.141
MA0080.21.93823e-9
MA0081.10.0043
MA0083.14.02576e-4
MA0084.10.511
MA0087.10.436
MA0088.10.662
MA0090.10.0105
MA0091.10.0121
MA0092.10.712
MA0093.10.321
MA0099.20.726
MA0100.10.301
MA0101.10.00688
MA0102.20.933
MA0103.10.114
MA0104.20.0948
MA0105.10.673
MA0106.10.433
MA0107.10.00588
MA0108.20.0671
MA0111.10.601
MA0112.20.0482
MA0113.10.0625
MA0114.10.802
MA0115.10.271
MA0116.10.876
MA0117.10.178
MA0119.10.505
MA0122.10.909
MA0124.10.491
MA0125.10.464
MA0131.10.44
MA0135.10.585
MA0136.19.22295e-13
MA0137.20.317
MA0138.20.189
MA0139.10.866
MA0140.10.0669
MA0141.10.301
MA0142.10.51
MA0143.10.814
MA0144.10.117
MA0145.10.317
MA0146.10.213
MA0147.10.0636
MA0148.10.13
MA0149.10.0601
MA0150.10.157
MA0152.10.04
MA0153.10.231
MA0154.10.521
MA0155.10.0912
MA0156.11.15336e-10
MA0157.10.775
MA0159.10.502
MA0160.10.363
MA0162.10.167
MA0163.10.239
MA0164.10.882
MA0258.10.901
MA0259.10.204



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: CNhs12064

Novel motifP-value
10.457
100.515
1000.424
1010.3
1020.299
1030.333
1040.695
1050.826
1060.378
1070.0355
1080.436
1090.996
110.681
1100.53
1110.279
1120.729
1130.94
1140.978
1150.399
1160.107
1170.736
1180.991
1190.898
120.533
1200.255
1210.243
1220.185
1233.18657e-5
1240.323
1250.0181
1260.697
1270.322
1280.0482
1290.769
130.108
1300.526
1310.208
1320.131
1330.811
1340.476
1350.764
1360.291
1370.107
1380.428
1390.864
140.986
1400.665
1410.0947
1420.457
1430.769
1440.434
1450.82
1460.808
1470.221
1480.914
1490.0671
150.391
1500.846
1510.734
1520.0853
1530.773
1540.206
1550.0846
1560.268
1570.681
1580.0599
1590.478
160.0641
1600.54
1610.638
1620.352
1630.964
1640.481
1650.894
1660.251
1670.107
1680.795
1690.141
170.391
180.515
190.0366
20.0862
200.382
210.579
220.0687
230.201
240.488
250.447
260.786
270.103
280.133
290.451
30.793
300.0704
310.28
323.16343e-10
330.805
340.468
350.739
360.0251
370.162
380.674
390.475
40.132
400.0762
410.102
420.526
430.992
440.401
450.138
460.477
470.335
480.701
490.506
50.846
500.521
510.636
520.402
530.0541
540.569
550.438
560.863
570.469
580.326
590.029
60.303
600.592
610.298
620.715
630.868
640.812
650.312
660.241
670.72
680.126
690.264
70.512
701
710.477
720.961
730.0841
740.305
750.814
760.55
770.0758
780.231
790.0243
80.516
800.68
810.722
820.341
830.929
840.286
850.24
860.725
870.624
880.469
890.212
90.134
900.00619
910.999
920.263
930.588
940.858
950.843
960.878
970.507
980.647
993.54481e-4



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: CNhs12064


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)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002602 (annulus pulposus cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000075 (subdivision of skeletal system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000982 (skeletal joint)
0001062 (anatomical entity)
0001066 (intervertebral disk)
0001130 (vertebral column)
0001137 (dorsum)
0001434 (skeletal system)
0001468 (intervertebral joint)
0001995 (fibrocartilage)
0002050 (embryonic structure)
0002100 (trunk)
0002204 (musculoskeletal system)
0002209 (fibrous joint)
0002213 (cartilaginous joint)
0002216 (symphysis)
0002329 (somite)
0002384 (connective tissue)
0002418 (cartilage tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003089 (sclerotome)
0003104 (mesenchyme)
0003586 (trunk connective tissue)
0004120 (mesoderm-derived structure)
0004288 (skeleton)
0004715 (annulus fibrosus disci intervertebralis)
0004755 (skeletal tissue)
0004765 (skeletal element)
0004770 (articular system)
0004905 (articulation)
0005174 (dorsal region element)
0005177 (trunk region element)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006444 (annulus fibrosus)
0009142 (entire embryonic mesenchyme)

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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