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FF:11409-118E5: 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 17:07, 29 March 2012


Name:Nucleus 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 typenucleus pulposus cell of intervertebral disc
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:4797
catalog numberSC4805
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-penis0
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-0.296
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: CNhs12019

Jaspar motifP-value
MA0002.20.698
MA0003.10.22
MA0004.10.568
MA0006.10.273
MA0007.10.165
MA0009.10.629
MA0014.10.516
MA0017.10.0782
MA0018.21.25573e-4
MA0019.10.768
MA0024.11.22021e-4
MA0025.10.00117
MA0027.10.894
MA0028.10.0177
MA0029.10.683
MA0030.10.309
MA0031.10.216
MA0035.20.381
MA0038.10.418
MA0039.20.299
MA0040.10.511
MA0041.10.348
MA0042.10.36
MA0043.11.47235e-4
MA0046.10.569
MA0047.20.895
MA0048.10.708
MA0050.14.34538e-4
MA0051.10.00546
MA0052.10.135
MA0055.10.417
MA0057.10.234
MA0058.10.552
MA0059.10.557
MA0060.13.4189e-5
MA0061.10.809
MA0062.21.74529e-7
MA0065.20.0176
MA0066.10.0735
MA0067.10.0148
MA0068.10.611
MA0069.10.221
MA0070.10.594
MA0071.10.548
MA0072.10.534
MA0073.10.392
MA0074.10.0366
MA0076.10.00108
MA0077.10.607
MA0078.10.694
MA0079.20.833
MA0080.26.20995e-7
MA0081.16.79201e-4
MA0083.10.0127
MA0084.10.212
MA0087.10.742
MA0088.10.58
MA0090.10.0261
MA0091.10.00991
MA0092.10.676
MA0093.10.462
MA0099.20.0601
MA0100.10.258
MA0101.10.0482
MA0102.20.282
MA0103.10.54
MA0104.20.228
MA0105.10.13
MA0106.10.471
MA0107.10.0473
MA0108.20.0606
MA0111.10.766
MA0112.20.0021
MA0113.10.0342
MA0114.10.166
MA0115.10.799
MA0116.10.0542
MA0117.10.229
MA0119.10.0778
MA0122.10.508
MA0124.10.29
MA0125.10.228
MA0131.10.166
MA0135.10.502
MA0136.14.28329e-11
MA0137.20.38
MA0138.20.108
MA0139.10.186
MA0140.10.127
MA0141.10.0887
MA0142.10.537
MA0143.10.168
MA0144.10.167
MA0145.10.281
MA0146.10.0493
MA0147.10.168
MA0148.10.328
MA0149.10.323
MA0150.10.0329
MA0152.10.222
MA0153.10.534
MA0154.10.0444
MA0155.10.163
MA0156.11.0212e-9
MA0157.10.385
MA0159.10.452
MA0160.10.929
MA0162.10.116
MA0163.10.00213
MA0164.10.736
MA0258.10.0485
MA0259.10.205



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: CNhs12019

Novel motifP-value
10.549
100.54
1000.973
1010.612
1020.371
1030.125
1040.604
1050.719
1060.056
1070.0197
1080.36
1090.646
110.152
1100.374
1110.95
1120.588
1130.149
1140.379
1150.131
1160.0272
1170.547
1180.818
1190.62
120.201
1200.0279
1210.168
1220.0893
1230.00254
1240.521
1250.679
1260.499
1270.456
1280.0118
1290.168
130.683
1300.577
1310.239
1320.158
1330.381
1340.776
1350.563
1360.859
1370.0326
1380.438
1390.243
140.856
1400.554
1410.354
1420.692
1430.468
1440.389
1450.435
1460.29
1470.469
1480.158
1490.0173
150.76
1500.611
1510.33
1520.233
1530.855
1540.299
1550.161
1560.319
1570.945
1580.137
1590.834
160.0348
1600.0813
1610.201
1620.0087
1630.653
1640.441
1650.93
1660.174
1670.414
1680.852
1690.0395
170.473
180.351
190.0269
20.14
200.448
210.526
220.0695
230.22
240.63
250.675
260.302
270.125
280.137
290.264
30.16
300.215
310.264
322.10357e-10
330.846
340.32
350.516
360.337
370.0787
380.858
390.273
40.152
400.579
410.0981
420.851
430.255
440.0339
450.245
460.0552
470.493
480.607
490.384
50.648
500.507
510.343
520.448
530.432
540.261
550.473
560.307
570.549
580.996
590.00377
60.522
600.496
610.746
620.559
630.326
640.499
650.0887
660.367
670.914
680.2
690.00558
70.765
700.243
710.174
720.795
730.0805
740.542
750.431
760.451
770.089
780.801
790.0122
80.0619
800.243
810.557
820.0168
830.807
840.448
850.11
860.775
870.853
880.222
890.0744
90.246
900.31
910.168
920.0969
930.675
940.707
950.408
960.5
970.568
980.704
993.57099e-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: CNhs12019


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)
0002564 (nucleus pulposus cell of intervertebral disc)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002242 (nucleus pulposus)
0002328 (notochord)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003068 (axial mesoderm)
0004120 (mesoderm-derived structure)
0004880 (chordamesoderm)
0005423 (developing anatomical structure)

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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