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FF:11411-118E7: 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:Chondrocyte - re diff, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecartilage
dev stage57 years old adult
sexmale
age57
cell typechondrocyte
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1737
catalog numberCA402RD-R10a
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-penis0.221
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-0.285
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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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: CNhs12021

Jaspar motifP-value
MA0002.20.0561
MA0003.10.397
MA0004.10.12
MA0006.10.214
MA0007.10.964
MA0009.10.378
MA0014.10.157
MA0017.10.0625
MA0018.20.609
MA0019.10.413
MA0024.10.00148
MA0025.10.507
MA0027.10.493
MA0028.10.0629
MA0029.10.0532
MA0030.10.316
MA0031.10.282
MA0035.20.00437
MA0038.10.158
MA0039.20.113
MA0040.10.669
MA0041.10.322
MA0042.10.944
MA0043.10.562
MA0046.10.184
MA0047.20.709
MA0048.10.00634
MA0050.10.147
MA0051.10.688
MA0052.10.146
MA0055.10.212
MA0057.10.501
MA0058.10.0596
MA0059.10.162
MA0060.13.76356e-5
MA0061.10.624
MA0062.21.16525e-5
MA0065.20.442
MA0066.10.631
MA0067.10.241
MA0068.10.691
MA0069.10.0528
MA0070.10.902
MA0071.10.849
MA0072.10.693
MA0073.10.544
MA0074.10.148
MA0076.10.0448
MA0077.10.268
MA0078.10.85
MA0079.20.489
MA0080.25.72177e-7
MA0081.10.00486
MA0083.10.292
MA0084.10.279
MA0087.10.386
MA0088.10.0279
MA0090.10.0134
MA0091.10.468
MA0092.10.579
MA0093.10.132
MA0099.20.0456
MA0100.10.111
MA0101.10.713
MA0102.20.601
MA0103.10.00326
MA0104.20.00533
MA0105.10.0478
MA0106.10.962
MA0107.10.833
MA0108.28.33314e-5
MA0111.10.0331
MA0112.20.208
MA0113.10.795
MA0114.10.0905
MA0115.10.0728
MA0116.10.914
MA0117.10.981
MA0119.10.904
MA0122.10.649
MA0124.10.12
MA0125.10.218
MA0131.10.83
MA0135.10.735
MA0136.16.82553e-8
MA0137.20.112
MA0138.20.324
MA0139.10.379
MA0140.10.00131
MA0141.10.749
MA0142.10.0293
MA0143.10.466
MA0144.10.28
MA0145.10.64
MA0146.10.394
MA0147.10.0152
MA0148.10.676
MA0149.10.283
MA0150.10.0978
MA0152.10.00229
MA0153.10.951
MA0154.10.653
MA0155.10.071
MA0156.18.39588e-7
MA0157.10.627
MA0159.10.511
MA0160.10.644
MA0162.10.221
MA0163.10.163
MA0164.10.425
MA0258.10.969
MA0259.10.782



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: CNhs12021

Novel motifP-value
10.253
100.524
1000.544
1010.121
1020.833
1030.759
1040.81
1050.00122
1060.245
1070.0455
1080.352
1090.711
110.622
1100.466
1110.881
1120.884
1130.122
1140.701
1150.0422
1160.0326
1170.321
1180.969
1190.353
120.423
1200.776
1210.223
1220.0537
1230.244
1240.0381
1250.758
1260.329
1270.699
1280.212
1290.298
130.714
1300.464
1310.749
1320.122
1330.432
1340.878
1350.614
1360.773
1370.448
1380.739
1390.306
140.364
1400.402
1410.408
1420.132
1430.57
1440.139
1450.428
1460.419
1470.617
1480.249
1490.00887
150.262
1500.3
1510.752
1520.0366
1530.696
1540.897
1550.892
1560.879
1570.311
1580.00743
1590.439
160.0968
1600.658
1610.658
1620.814
1630.911
1640.089
1650.815
1660.0161
1670.749
1680.325
1690.103
170.922
180.751
190.0169
20.198
200.795
210.801
220.237
230.314
240.071
250.155
260.599
270.552
280.142
290.271
30.539
300.561
310.593
323.68898e-12
330.44
340.467
350.427
360.0486
370.701
380.632
390.604
40.852
400.356
410.166
420.287
430.865
440.7
450.463
460.873
470.038
480.394
490.47
50.906
500.522
510.403
520.538
530.134
540.483
550.905
560.965
570.299
580.214
590.0213
60.213
600.447
610.59
620.374
630.719
640.329
650.458
660.0374
670.79
680.683
690.387
70.416
700.465
710.356
720.33
730.0141
740.453
750.633
760.355
770.00305
780.249
790.00263
80.756
800.159
810.762
820.705
830.0478
840.892
850.133
860.647
870.386
880.361
890.0729
90.788
900.133
910.886
920.581
930.682
940.31
950.754
960.858
970.483
980.989
990.301



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: CNhs12021


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000058 (chondroblast)
0000134 (mesenchymal cell)
0000138 (chondrocyte)
0000151 (secretory cell)
0000153 (GAG secreting cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000327 (extracellular matrix secreting cell)
0000447 (carbohydrate secreting cell)
0000499 (stromal cell)
0000548 (animal cell)
0000667 (collagen secreting cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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