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FF:11763-123H8: 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 17:23, 29 March 2012


Name:tenocyte, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuetendon
dev stageNA
sexNA
ageNA
cell typetenocyte
cell lineNA
companyNA
collaborationGundula Schulze-Tanzil
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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-penis0.131
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-lymphoma0.0594
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12639

Jaspar motifP-value
MA0002.20.339
MA0003.10.153
MA0004.10.143
MA0006.10.159
MA0007.10.391
MA0009.10.723
MA0014.10.295
MA0017.10.687
MA0018.27.18615e-6
MA0019.10.826
MA0024.10.028
MA0025.18.19682e-5
MA0027.10.698
MA0028.16.70943e-4
MA0029.10.63
MA0030.10.04
MA0031.10.125
MA0035.20.0108
MA0038.10.0159
MA0039.20.0189
MA0040.10.914
MA0041.10.596
MA0042.10.876
MA0043.11.69978e-6
MA0046.10.125
MA0047.20.539
MA0048.10.251
MA0050.10.828
MA0051.10.807
MA0052.10.0111
MA0055.10.9
MA0057.10.218
MA0058.10.0509
MA0059.10.943
MA0060.18.05676e-8
MA0061.10.869
MA0062.21.98279e-11
MA0065.20.442
MA0066.10.254
MA0067.18.60774e-4
MA0068.10.186
MA0069.10.254
MA0070.10.534
MA0071.10.701
MA0072.10.24
MA0073.10.947
MA0074.10.0623
MA0076.15.23971e-5
MA0077.10.387
MA0078.10.731
MA0079.20.748
MA0080.22.37553e-8
MA0081.10.00455
MA0083.10.715
MA0084.10.27
MA0087.10.783
MA0088.10.848
MA0090.10.118
MA0091.10.0251
MA0092.10.317
MA0093.10.104
MA0099.22.39216e-5
MA0100.10.687
MA0101.10.049
MA0102.20.133
MA0103.10.144
MA0104.20.0681
MA0105.10.292
MA0106.10.0609
MA0107.10.0637
MA0108.20.623
MA0111.10.95
MA0112.23.23149e-4
MA0113.10.812
MA0114.10.912
MA0115.10.802
MA0116.10.0289
MA0117.10.193
MA0119.10.194
MA0122.10.285
MA0124.10.0574
MA0125.10.2
MA0131.10.0816
MA0135.10.61
MA0136.14.70391e-13
MA0137.20.673
MA0138.20.074
MA0139.10.806
MA0140.10.0469
MA0141.10.249
MA0142.10.27
MA0143.10.443
MA0144.10.846
MA0145.10.15
MA0146.10.533
MA0147.10.183
MA0148.10.781
MA0149.10.912
MA0150.10.00252
MA0152.10.0128
MA0153.10.49
MA0154.10.0978
MA0155.10.148
MA0156.11.74746e-11
MA0157.10.743
MA0159.10.714
MA0160.10.318
MA0162.10.0654
MA0163.12.18302e-4
MA0164.10.917
MA0258.10.0836
MA0259.10.11



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: CNhs12639

Novel motifP-value
10.424
100.526
1000.55
1010.306
1020.237
1030.0777
1040.804
1050.114
1060.225
1070.0316
1080.301
1090.412
110.271
1100.23
1110.697
1120.553
1130.0174
1140.188
1150.0339
1160.0586
1170.985
1180.932
1190.626
120.235
1200.652
1210.48
1220.0219
1230.0165
1240.718
1250.686
1260.864
1270.822
1280.0797
1290.611
130.639
1300.536
1310.79
1320.236
1330.142
1340.635
1350.504
1360.759
1370.599
1380.744
1390.636
140.509
1400.725
1410.46
1420.779
1430.661
1440.29
1450.754
1460.987
1470.297
1480.808
1490.0169
150.786
1500.215
1510.486
1520.132
1530.986
1540.846
1550.2
1560.532
1570.349
1580.0123
1590.628
160.00627
1600.351
1610.938
1620.245
1630.871
1640.142
1650.841
1660.0452
1670.454
1680.649
1690.019
170.351
180.361
190.00191
20.2
200.333
210.0379
220.273
230.155
240.329
250.474
260.217
270.355
280.238
290.248
30.427
300.434
310.443
325.53423e-20
330.884
340.584
350.833
360.05
370.0973
380.912
390.268
40.833
400.229
410.282
420.75
430.426
440.067
450.733
460.161
470.912
480.79
490.962
50.996
500.532
510.642
520.583
530.191
540.651
550.423
560.791
570.97
580.45
590.0107
60.31
600.6
610.789
620.824
630.196
640.785
650.327
660.229
670.852
680.395
690.515
70.495
700.32
710.389
720.799
730.111
740.246
750.849
760.966
770.0389
780.544
795.70064e-5
80.0859
800.0945
810.391
820.433
830.298
840.311
850.258
860.489
870.273
880.42
890.0392
90.517
900.875
910.535
920.236
930.44
940.663
950.994
960.861
970.325
980.97
990.00177



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: CNhs12639


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)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000135 (fibrocyte)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000386 (attachment cell)
0000388 (tendon cell)
0000499 (stromal cell)
0000548 (animal cell)
0000630 (supportive cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000043 (tendon)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002384 (connective tissue)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0005423 (developing anatomical structure)

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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