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FF:11410-118E6: 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 - de 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 stage56 years old adult
sexmale
age56
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 number2230
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-penis0.2
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-0.169
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: CNhs12020

Jaspar motifP-value
MA0002.20.0175
MA0003.10.293
MA0004.10.0998
MA0006.10.106
MA0007.10.516
MA0009.10.329
MA0014.10.333
MA0017.10.876
MA0018.20.00139
MA0019.10.99
MA0024.10.00553
MA0025.10.0247
MA0027.10.465
MA0028.10.00298
MA0029.10.689
MA0030.10.0634
MA0031.10.139
MA0035.20.00456
MA0038.10.0233
MA0039.20.0209
MA0040.10.882
MA0041.10.41
MA0042.10.906
MA0043.18.34298e-4
MA0046.10.144
MA0047.20.741
MA0048.10.0305
MA0050.10.114
MA0051.10.441
MA0052.10.0961
MA0055.10.777
MA0057.10.184
MA0058.10.0279
MA0059.10.289
MA0060.11.91328e-12
MA0061.10.067
MA0062.22.28332e-10
MA0065.20.964
MA0066.10.605
MA0067.10.0032
MA0068.10.325
MA0069.10.15
MA0070.10.614
MA0071.10.581
MA0072.10.0618
MA0073.10.948
MA0074.10.476
MA0076.14.41516e-4
MA0077.10.0404
MA0078.10.762
MA0079.20.783
MA0080.21.48203e-9
MA0081.10.00101
MA0083.10.171
MA0084.10.643
MA0087.10.361
MA0088.10.29
MA0090.10.00531
MA0091.10.321
MA0092.10.523
MA0093.10.0785
MA0099.21.14115e-7
MA0100.10.214
MA0101.11.92003e-4
MA0102.20.338
MA0103.10.0326
MA0104.20.0135
MA0105.10.136
MA0106.10.483
MA0107.14.12988e-4
MA0108.20.161
MA0111.10.446
MA0112.20.0105
MA0113.10.578
MA0114.10.68
MA0115.10.726
MA0116.10.274
MA0117.10.351
MA0119.10.478
MA0122.10.366
MA0124.10.211
MA0125.10.117
MA0131.10.278
MA0135.10.218
MA0136.11.76161e-12
MA0137.20.474
MA0138.20.345
MA0139.10.521
MA0140.10.00582
MA0141.10.116
MA0142.10.0218
MA0143.10.661
MA0144.10.832
MA0145.10.253
MA0146.10.193
MA0147.10.0306
MA0148.10.727
MA0149.10.975
MA0150.10.00136
MA0152.10.0527
MA0153.10.806
MA0154.10.763
MA0155.10.252
MA0156.16.91475e-12
MA0157.10.377
MA0159.10.593
MA0160.10.859
MA0162.10.0844
MA0163.10.0281
MA0164.10.813
MA0258.10.58
MA0259.10.176



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: CNhs12020

Novel motifP-value
10.703
100.564
1000.949
1010.22
1020.123
1030.689
1040.891
1050.0224
1060.564
1070.0461
1080.157
1090.602
110.775
1100.995
1110.692
1120.99
1130.781
1140.278
1150.00101
1160.0111
1170.346
1180.734
1190.474
120.147
1200.662
1210.266
1220.0441
1230.0376
1240.0908
1250.616
1260.657
1270.706
1280.412
1290.315
130.844
1300.314
1310.518
1320.0229
1330.588
1340.329
1350.695
1360.368
1370.278
1380.501
1390.19
140.341
1400.348
1410.313
1420.617
1430.645
1440.331
1450.806
1460.0972
1470.468
1480.423
1490.0075
150.51
1500.485
1510.797
1520.0117
1530.656
1540.575
1550.729
1560.691
1570.59
1580.0378
1590.899
160.0824
1600.658
1610.581
1620.479
1630.841
1640.0386
1650.426
1660.00839
1670.691
1680.463
1690.0228
170.807
180.707
190.00427
20.303
200.631
210.0366
220.16
230.531
240.0801
250.396
260.895
270.651
280.116
290.17
30.755
300.609
310.636
324.03407e-14
330.706
340.539
350.722
360.0143
370.262
380.636
390.496
40.515
400.13
410.199
420.658
430.906
440.189
450.76
460.725
470.329
480.856
490.554
50.927
500.568
510.807
520.86
530.0965
540.753
550.752
560.995
570.927
580.242
590.0549
60.308
600.747
610.434
620.613
630.321
640.482
650.403
660.0418
670.997
680.569
690.281
70.379
700.223
710.861
720.406
730.00421
740.277
750.68
760.33
776.89005e-4
780.104
799.56579e-4
80.164
800.0136
810.656
820.16
830.597
840.606
850.126
860.895
870.924
880.207
890.0731
90.816
900.228
910.742
920.577
930.831
940.848
950.479
960.897
970.67
980.845
990.0248



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: CNhs12020


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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