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FF:11261-116G1: 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 17:01, 29 March 2012


Name:Chondrocyte - de diff, donor1
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 typechondroblast
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 numberCA402-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-penis0.0142
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-lymphoma0.415
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: CNhs11923

Jaspar motifP-value
MA0002.20.0207
MA0003.10.31
MA0004.10.008
MA0006.10.131
MA0007.10.962
MA0009.10.578
MA0014.10.391
MA0017.10.854
MA0018.20.00136
MA0019.10.926
MA0024.10.144
MA0025.10.112
MA0027.10.282
MA0028.10.963
MA0029.10.872
MA0030.10.0315
MA0031.10.0682
MA0035.20.0132
MA0038.10.299
MA0039.20.2
MA0040.10.927
MA0041.10.97
MA0042.10.905
MA0043.10.0125
MA0046.10.0797
MA0047.20.744
MA0048.13.7956e-4
MA0050.10.581
MA0051.10.792
MA0052.10.0405
MA0055.10.0326
MA0057.10.215
MA0058.17.99073e-4
MA0059.10.2
MA0060.17.47884e-5
MA0061.10.0321
MA0062.20.00209
MA0065.20.813
MA0066.10.916
MA0067.10.0414
MA0068.10.0604
MA0069.10.493
MA0070.10.703
MA0071.10.902
MA0072.10.222
MA0073.10.639
MA0074.10.853
MA0076.10.585
MA0077.10.0748
MA0078.10.201
MA0079.20.508
MA0080.22.87485e-10
MA0081.18.67254e-4
MA0083.10.502
MA0084.10.818
MA0087.10.167
MA0088.10.53
MA0090.10.00208
MA0091.10.809
MA0092.10.417
MA0093.10.00433
MA0099.21.77579e-6
MA0100.10.382
MA0101.11.97672e-4
MA0102.20.0326
MA0103.13.60959e-4
MA0104.20.00258
MA0105.10.112
MA0106.10.193
MA0107.13.35018e-4
MA0108.20.934
MA0111.10.51
MA0112.20.0178
MA0113.10.883
MA0114.10.532
MA0115.10.962
MA0116.10.0989
MA0117.10.347
MA0119.10.509
MA0122.10.258
MA0124.10.524
MA0125.10.0873
MA0131.10.388
MA0135.10.164
MA0136.11.81605e-10
MA0137.20.196
MA0138.20.878
MA0139.10.595
MA0140.10.0207
MA0141.10.265
MA0142.10.00207
MA0143.10.95
MA0144.10.12
MA0145.10.234
MA0146.10.335
MA0147.10.0134
MA0148.10.55
MA0149.10.401
MA0150.10.00134
MA0152.10.0225
MA0153.10.802
MA0154.10.754
MA0155.10.789
MA0156.12.61882e-8
MA0157.10.26
MA0159.10.251
MA0160.10.338
MA0162.10.0353
MA0163.10.0505
MA0164.10.9
MA0258.10.79
MA0259.10.227



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: CNhs11923

Novel motifP-value
10.618
100.0932
1000.149
1010.403
1020.267
1030.434
1040.456
1050.249
1060.0467
1070.302
1080.586
1090.449
110.444
1100.258
1110.766
1120.834
1130.00573
1140.477
1150.00589
1160.0268
1170.359
1180.772
1190.484
120.0654
1200.748
1210.388
1220.0434
1230.0216
1240.242
1250.342
1260.58
1270.91
1280.571
1290.641
130.0709
1300.678
1310.625
1320.0358
1330.361
1340.443
1350.967
1360.689
1370.467
1380.178
1390.406
140.198
1400.12
1410.115
1420.663
1430.211
1440.561
1450.445
1460.0537
1470.199
1480.642
1490.0191
150.368
1500.313
1510.373
1520.13
1530.567
1540.247
1550.486
1560.376
1570.304
1580.00694
1590.37
160.109
1600.914
1610.969
1620.974
1630.267
1640.123
1650.604
1660.00171
1670.634
1680.834
1690.00818
170.658
180.828
190.00213
20.697
200.891
210.00569
220.214
230.279
240.15
250.595
260.887
270.709
280.377
290.16
30.997
300.516
310.771
321.01914e-12
330.972
340.984
350.121
360.307
370.565
380.982
390.259
40.332
400.759
410.116
420.545
430.694
440.353
450.456
460.726
470.408
480.766
490.575
50.752
500.441
510.916
520.302
530.347
540.973
550.843
560.557
570.526
580.557
590.144
60.36
600.582
610.64
620.86
630.289
640.888
650.357
660.552
670.542
680.923
690.224
70.35
700.966
710.35
720.208
730.059
740.115
750.783
760.466
770.00222
780.039
790.0145
80.183
800.14
810.99
820.886
830.534
840.333
850.603
860.949
870.589
880.393
890.328
90.6
900.447
910.362
920.562
930.89
940.574
950.831
960.871
970.563
980.781
990.117



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: CNhs11923


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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