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FF:11338-117F6: 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 - de 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 typechondroblast
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 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-penis-0.166
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-0.284
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
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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: CNhs11372

Jaspar motifP-value
MA0002.20.957
MA0003.10.165
MA0004.10.487
MA0006.10.198
MA0007.10.932
MA0009.10.127
MA0014.10.346
MA0017.10.887
MA0018.26.39224e-4
MA0019.10.647
MA0024.14.19831e-5
MA0025.10.331
MA0027.10.537
MA0028.10.0604
MA0029.10.535
MA0030.10.664
MA0031.10.602
MA0035.20.158
MA0038.10.0406
MA0039.20.257
MA0040.10.359
MA0041.10.236
MA0042.10.414
MA0043.10.00189
MA0046.10.316
MA0047.20.308
MA0048.10.291
MA0050.10.0205
MA0051.10.683
MA0052.10.946
MA0055.10.921
MA0057.10.426
MA0058.10.432
MA0059.10.7
MA0060.19.66956e-8
MA0061.10.5
MA0062.22.69705e-6
MA0065.20.921
MA0066.10.481
MA0067.10.0327
MA0068.10.713
MA0069.10.141
MA0070.10.945
MA0071.10.306
MA0072.10.6
MA0073.10.799
MA0074.10.697
MA0076.10.019
MA0077.10.184
MA0078.10.563
MA0079.20.936
MA0080.28.49596e-9
MA0081.10.00154
MA0083.10.00143
MA0084.10.792
MA0087.10.776
MA0088.10.846
MA0090.11.96332e-5
MA0091.10.0552
MA0092.10.113
MA0093.10.459
MA0099.20.746
MA0100.10.417
MA0101.10.0419
MA0102.20.4
MA0103.10.00767
MA0104.20.114
MA0105.10.604
MA0106.10.0338
MA0107.10.0725
MA0108.20.00241
MA0111.10.133
MA0112.26.00625e-4
MA0113.10.334
MA0114.10.685
MA0115.10.365
MA0116.10.576
MA0117.10.539
MA0119.10.382
MA0122.10.714
MA0124.10.688
MA0125.10.466
MA0131.10.206
MA0135.10.698
MA0136.13.73614e-8
MA0137.20.877
MA0138.20.27
MA0139.10.787
MA0140.10.322
MA0141.10.211
MA0142.10.144
MA0143.10.843
MA0144.10.855
MA0145.10.102
MA0146.10.232
MA0147.10.175
MA0148.10.253
MA0149.10.666
MA0150.10.2
MA0152.10.056
MA0153.10.117
MA0154.10.177
MA0155.10.0674
MA0156.19.97812e-7
MA0157.10.301
MA0159.10.469
MA0160.10.998
MA0162.10.0585
MA0163.10.135
MA0164.10.729
MA0258.10.218
MA0259.10.355



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: CNhs11372

Novel motifP-value
10.738
100.833
1000.781
1010.118
1020.0624
1030.114
1040.556
1050.688
1060.201
1070.0209
1080.22
1090.605
110.542
1100.73
1110.281
1120.626
1130.251
1140.233
1150.201
1160.0323
1170.283
1180.798
1190.602
120.377
1200.638
1210.605
1220.876
1230.0014
1240.53
1250.895
1260.466
1270.665
1280.335
1290.908
130.838
1300.618
1310.669
1320.156
1330.487
1340.0712
1350.112
1360.419
1370.535
1380.421
1390.35
140.599
1400.116
1410.507
1420.714
1430.644
1440.369
1450.649
1460.587
1470.459
1480.0938
1490.00411
150.722
1500.636
1510.588
1520.0216
1530.424
1540.907
1550.177
1560.83
1570.172
1580.00909
1590.343
160.0532
1600.45
1610.938
1620.69
1630.62
1640.275
1650.866
1666.64788e-4
1670.24
1680.8
1690.0159
170.583
180.0821
190.0078
20.426
200.165
210.427
220.064
230.0914
240.116
250.536
260.776
270.62
280.209
290.557
30.966
300.0914
310.518
323.88982e-14
330.823
340.377
350.863
360.0993
370.324
380.932
390.232
40.636
400.777
410.548
420.675
430.219
440.749
450.411
460.344
470.641
480.91
490.617
50.356
500.374
510.641
520.413
530.28
540.405
550.797
560.786
570.724
580.479
590.0339
60.404
600.535
610.54
620.729
630.239
640.782
650.148
660.24
670.674
680.373
690.0976
70.955
700.0389
710.48
720.593
730.0192
740.611
750.767
760.929
770.0128
780.152
790.0176
80.205
800.969
810.465
820.181
830.617
840.301
850.0195
860.491
870.22
880.187
890.0219
90.344
900.178
910.917
920.365
930.71
940.613
950.655
960.943
970.417
980.488
990.0214



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: CNhs11372


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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