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FF:11765-123I1: 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, donor2
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-penis0.18
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-0.287
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: CNhs12640

Jaspar motifP-value
MA0002.20.164
MA0003.10.153
MA0004.10.156
MA0006.10.238
MA0007.10.777
MA0009.10.495
MA0014.10.582
MA0017.10.473
MA0018.21.86588e-5
MA0019.10.37
MA0024.12.3607e-4
MA0025.12.62952e-4
MA0027.10.455
MA0028.10.0078
MA0029.10.626
MA0030.10.188
MA0031.10.901
MA0035.20.00424
MA0038.10.0422
MA0039.20.293
MA0040.10.821
MA0041.10.459
MA0042.10.529
MA0043.11.14176e-5
MA0046.10.221
MA0047.20.933
MA0048.10.177
MA0050.10.165
MA0051.10.0722
MA0052.10.709
MA0055.10.625
MA0057.10.197
MA0058.10.13
MA0059.10.34
MA0060.13.64986e-11
MA0061.10.212
MA0062.22.20547e-9
MA0065.20.564
MA0066.10.239
MA0067.10.0238
MA0068.10.897
MA0069.10.339
MA0070.10.47
MA0071.10.856
MA0072.10.476
MA0073.10.641
MA0074.10.169
MA0076.10.00127
MA0077.10.114
MA0078.10.87
MA0079.20.998
MA0080.28.68411e-8
MA0081.10.00243
MA0083.10.293
MA0084.10.243
MA0087.10.525
MA0088.10.834
MA0090.10.00155
MA0091.10.0269
MA0092.10.371
MA0093.10.136
MA0099.21.15532e-5
MA0100.10.155
MA0101.18.72647e-4
MA0102.20.577
MA0103.10.00977
MA0104.20.0406
MA0105.10.437
MA0106.10.282
MA0107.10.00252
MA0108.20.0405
MA0111.10.409
MA0112.20.00173
MA0113.10.564
MA0114.10.747
MA0115.10.529
MA0116.10.14
MA0117.10.0793
MA0119.10.397
MA0122.10.541
MA0124.10.706
MA0125.10.242
MA0131.10.197
MA0135.10.46
MA0136.15.89588e-12
MA0137.20.0431
MA0138.20.128
MA0139.10.387
MA0140.10.0132
MA0141.10.313
MA0142.10.179
MA0143.10.256
MA0144.10.112
MA0145.10.384
MA0146.10.199
MA0147.10.0361
MA0148.10.505
MA0149.10.964
MA0150.10.00966
MA0152.10.00451
MA0153.10.542
MA0154.10.268
MA0155.10.129
MA0156.11.05923e-9
MA0157.10.472
MA0159.10.624
MA0160.10.483
MA0162.10.0568
MA0163.10.0157
MA0164.10.9
MA0258.10.182
MA0259.10.0443



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: CNhs12640

Novel motifP-value
10.745
100.837
1000.945
1010.325
1020.0335
1030.368
1040.918
1050.0723
1060.464
1070.112
1080.396
1090.47
110.603
1100.418
1110.725
1120.51
1130.916
1140.399
1150.00535
1160.085
1170.596
1180.85
1190.523
120.199
1200.954
1210.534
1220.128
1230.00251
1240.334
1250.571
1260.68
1270.645
1280.237
1290.921
130.684
1300.601
1310.971
1320.0761
1330.419
1340.605
1350.759
1360.545
1370.631
1380.491
1390.715
140.677
1400.565
1410.296
1420.907
1430.964
1440.0888
1450.954
1460.502
1470.731
1480.418
1490.00223
150.418
1500.41
1510.385
1520.0712
1530.932
1540.454
1550.355
1560.517
1570.561
1580.0125
1590.495
160.0227
1600.47
1610.621
1620.374
1630.894
1640.246
1650.452
1660.00256
1670.436
1680.627
1690.0305
170.653
180.524
190.00265
20.155
200.49
210.0772
220.115
230.261
240.144
250.446
260.541
270.495
280.191
290.418
30.57
300.155
310.636
325.63663e-20
330.644
340.416
350.926
360.0438
370.147
380.772
390.223
40.145
400.704
410.265
420.765
430.605
440.337
450.566
460.576
470.508
480.977
490.838
50.902
500.292
510.759
520.495
530.302
540.6
550.683
560.947
570.83
580.335
590.0155
60.196
600.67
610.531
620.834
630.276
640.656
650.259
660.0714
670.802
680.662
690.456
70.208
700.111
710.933
720.549
730.0285
740.444
750.733
760.666
770.00205
780.19
791.068e-4
80.432
800.0964
810.74
820.267
830.297
840.221
850.167
860.851
870.673
880.208
890.0365
90.294
900.283
910.728
920.359
930.696
940.542
950.968
960.482
970.318
980.629
990.00656



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: CNhs12640


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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