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FF:11339-117F7: 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 16:47, 29 March 2012


Name:Chondrocyte - re diff, donor2
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 stage60 years old adult
sexmale
age60
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 number1662
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-penis-0.216
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-lymphoma0.168
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11373

Jaspar motifP-value
MA0002.20.314
MA0003.10.216
MA0004.10.0529
MA0006.10.194
MA0007.10.508
MA0009.10.125
MA0014.10.13
MA0017.10.767
MA0018.20.00229
MA0019.10.83
MA0024.10.166
MA0025.10.063
MA0027.10.715
MA0028.10.262
MA0029.10.105
MA0030.10.464
MA0031.10.554
MA0035.20.00196
MA0038.10.546
MA0039.20.0466
MA0040.10.9
MA0041.10.449
MA0042.10.963
MA0043.10.0111
MA0046.10.906
MA0047.20.212
MA0048.10.927
MA0050.10.00104
MA0051.10.0497
MA0052.10.465
MA0055.10.478
MA0057.10.528
MA0058.10.0698
MA0059.10.687
MA0060.10.0283
MA0061.10.744
MA0062.20.00101
MA0065.20.798
MA0066.10.876
MA0067.10.077
MA0068.10.14
MA0069.10.117
MA0070.10.587
MA0071.10.719
MA0072.10.96
MA0073.10.333
MA0074.10.954
MA0076.10.0846
MA0077.10.104
MA0078.10.965
MA0079.20.294
MA0080.20.00805
MA0081.10.135
MA0083.10.768
MA0084.10.443
MA0087.10.476
MA0088.10.622
MA0090.10.369
MA0091.10.0582
MA0092.10.104
MA0093.10.0904
MA0099.28.60763e-4
MA0100.10.888
MA0101.10.662
MA0102.20.0897
MA0103.10.00288
MA0104.20.0993
MA0105.10.177
MA0106.10.948
MA0107.10.645
MA0108.20.00632
MA0111.10.311
MA0112.27.03694e-4
MA0113.10.172
MA0114.10.671
MA0115.10.39
MA0116.10.0375
MA0117.10.761
MA0119.10.486
MA0122.10.727
MA0124.10.736
MA0125.10.404
MA0131.10.34
MA0135.10.453
MA0136.10.0534
MA0137.20.109
MA0138.20.282
MA0139.10.644
MA0140.10.194
MA0141.10.674
MA0142.10.25
MA0143.10.905
MA0144.10.315
MA0145.10.03
MA0146.10.745
MA0147.10.21
MA0148.10.0563
MA0149.10.636
MA0150.10.943
MA0152.13.60193e-5
MA0153.10.2
MA0154.10.0269
MA0155.10.268
MA0156.10.0359
MA0157.10.779
MA0159.10.4
MA0160.10.79
MA0162.10.236
MA0163.11.07245e-4
MA0164.10.583
MA0258.10.27
MA0259.10.393



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: CNhs11373

Novel motifP-value
10.58
100.855
1000.459
1010.88
1020.159
1030.0134
1040.449
1050.0042
1060.267
1070.0195
1080.975
1090.675
110.379
1100.641
1110.826
1120.34
1130.495
1140.23
1150.859
1160.119
1170.396
1180.238
1190.867
120.944
1200.886
1210.412
1220.2
1230.121
1240.59
1250.815
1260.892
1270.959
1280.0339
1290.854
130.596
1300.652
1310.11
1320.811
1330.61
1340.324
1350.178
1360.0595
1370.896
1380.562
1390.456
140.482
1400.55
1410.366
1420.301
1430.466
1440.336
1450.862
1460.234
1470.815
1480.487
1490.00526
150.0848
1500.57
1510.415
1520.277
1530.819
1540.776
1550.223
1560.985
1570.755
1580.053
1590.292
160.0608
1600.874
1610.552
1620.812
1630.577
1640.401
1650.415
1660.0163
1670.86
1680.63
1690.0113
170.634
180.19
190.0294
20.156
200.0459
210.462
220.172
230.0557
240.775
250.731
260.998
270.248
280.92
290.924
30.461
300.263
310.783
321.81672e-7
330.834
340.166
350.501
360.687
370.539
380.563
390.275
40.448
400.969
410.717
420.929
430.326
440.734
450.306
460.254
470.939
480.586
490.546
50.144
500.898
510.586
520.336
530.787
540.591
550.356
560.882
570.643
580.916
590.0187
60.295
600.137
610.696
620.32
630.482
640.959
650.282
660.853
670.383
680.678
690.559
70.178
700.356
710.141
720.662
730.481
740.304
750.966
760.666
770.00168
780.714
790.00692
80.486
800.237
810.497
820.27
830.667
840.404
850.071
860.213
870.556
880.223
890.131
90.082
900.566
910.38
920.106
930.0589
940.41
950.413
960.247
970.0885
980.967
990.187



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: CNhs11373


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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