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FF:11462-119B4: 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:Nucleus Pulposus Cell, donor3
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
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:5299
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-penis-0.142
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-0.272
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs12063

Jaspar motifP-value
MA0002.20.447
MA0003.10.315
MA0004.10.212
MA0006.10.941
MA0007.10.457
MA0009.10.456
MA0014.10.74
MA0017.10.296
MA0018.22.60967e-4
MA0019.10.763
MA0024.11.43226e-4
MA0025.10.314
MA0027.10.745
MA0028.10.208
MA0029.10.564
MA0030.10.222
MA0031.10.163
MA0035.20.556
MA0038.10.494
MA0039.20.271
MA0040.10.121
MA0041.10.386
MA0042.10.324
MA0043.10.0732
MA0046.10.198
MA0047.20.586
MA0048.10.102
MA0050.10.00172
MA0051.10.078
MA0052.10.68
MA0055.10.354
MA0057.10.878
MA0058.10.284
MA0059.10.421
MA0060.14.09376e-6
MA0061.10.9
MA0062.22.20804e-5
MA0065.20.292
MA0066.10.408
MA0067.10.0109
MA0068.10.376
MA0069.10.977
MA0070.10.414
MA0071.10.151
MA0072.10.703
MA0073.10.668
MA0074.10.15
MA0076.10.0576
MA0077.10.338
MA0078.10.916
MA0079.20.743
MA0080.21.9446e-8
MA0081.10.0109
MA0083.12.49335e-4
MA0084.10.533
MA0087.10.537
MA0088.10.838
MA0090.10.0101
MA0091.10.0382
MA0092.10.948
MA0093.10.309
MA0099.20.559
MA0100.10.338
MA0101.10.0741
MA0102.20.156
MA0103.10.565
MA0104.20.552
MA0105.10.309
MA0106.10.0519
MA0107.10.0704
MA0108.20.668
MA0111.10.605
MA0112.20.0195
MA0113.10.0498
MA0114.10.539
MA0115.10.115
MA0116.10.468
MA0117.10.23
MA0119.10.0771
MA0122.10.703
MA0124.10.244
MA0125.10.871
MA0131.10.249
MA0135.10.707
MA0136.13.41321e-11
MA0137.20.515
MA0138.20.346
MA0139.10.268
MA0140.10.402
MA0141.10.0398
MA0142.10.727
MA0143.10.38
MA0144.10.246
MA0145.10.787
MA0146.10.196
MA0147.10.82
MA0148.10.27
MA0149.10.109
MA0150.10.15
MA0152.10.0242
MA0153.10.386
MA0154.10.438
MA0155.10.148
MA0156.15.49648e-9
MA0157.10.556
MA0159.10.766
MA0160.10.651
MA0162.10.0608
MA0163.10.0208
MA0164.10.772
MA0258.10.559
MA0259.10.709



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: CNhs12063

Novel motifP-value
10.751
100.728
1000.965
1010.284
1020.4
1030.102
1040.441
1050.555
1060.199
1070.0054
1080.159
1090.239
110.115
1100.251
1110.971
1120.98
1130.365
1140.917
1150.643
1160.0116
1170.563
1180.662
1190.772
120.298
1200.0291
1210.275
1220.0951
1230.0025
1240.558
1250.497
1260.457
1270.914
1280.104
1290.603
130.483
1300.484
1310.531
1320.0909
1330.682
1340.272
1350.418
1360.712
1370.0243
1380.662
1390.323
140.688
1400.375
1410.051
1420.3
1430.437
1440.897
1450.312
1460.388
1470.227
1480.877
1490.073
150.839
1500.708
1510.655
1520.203
1530.935
1540.0654
1550.284
1560.285
1570.739
1580.198
1590.299
160.06
1600.179
1610.684
1620.153
1630.887
1640.141
1650.221
1660.442
1670.27
1680.712
1690.0901
170.0991
180.0329
190.029
20.193
200.876
210.571
220.101
230.105
240.941
250.603
260.586
270.107
280.0639
290.118
30.243
300.168
310.354
326.3502e-10
330.168
340.576
350.494
360.178
370.0617
380.908
390.475
40.0927
400.96
410.0677
420.812
430.519
440.076
450.456
460.148
470.956
480.755
490.564
50.779
500.611
510.61
520.486
530.115
540.417
550.621
560.343
570.783
580.436
590.0191
60.661
600.445
610.755
620.935
630.527
640.778
650.148
660.786
670.881
680.34
690.0553
70.687
700.272
710.634
720.539
730.04
740.885
750.5
760.561
770.0489
780.813
790.182
80.0871
800.96
810.786
820.436
830.823
840.501
850.156
860.791
870.981
880.69
890.0135
90.133
900.439
910.685
920.0652
930.28
940.17
950.245
960.598
970.52
980.389
993.64488e-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: CNhs12063


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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