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FF:11768-123I4: 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 17:24, 29 March 2012


Name:tenocyte, donor3
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-penis0.0701
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-0.023
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
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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: CNhs12641

Jaspar motifP-value
MA0002.20.417
MA0003.10.176
MA0004.10.0853
MA0006.10.363
MA0007.10.716
MA0009.10.39
MA0014.10.856
MA0017.10.703
MA0018.24.5175e-7
MA0019.10.481
MA0024.10.00781
MA0025.14.12392e-4
MA0027.10.962
MA0028.10.0234
MA0029.10.378
MA0030.10.0332
MA0031.10.16
MA0035.20.0166
MA0038.10.00917
MA0039.20.128
MA0040.10.632
MA0041.10.574
MA0042.10.747
MA0043.12.73736e-7
MA0046.10.0864
MA0047.20.501
MA0048.10.176
MA0050.10.068
MA0051.10.405
MA0052.10.0781
MA0055.10.923
MA0057.10.223
MA0058.10.0385
MA0059.10.965
MA0060.11.32834e-9
MA0061.10.625
MA0062.22.26537e-7
MA0065.20.287
MA0066.10.148
MA0067.10.00321
MA0068.10.0689
MA0069.10.0747
MA0070.10.723
MA0071.10.734
MA0072.10.413
MA0073.10.562
MA0074.10.361
MA0076.10.00238
MA0077.10.335
MA0078.10.708
MA0079.20.571
MA0080.21.3608e-7
MA0081.10.00634
MA0083.10.831
MA0084.10.332
MA0087.10.881
MA0088.10.593
MA0090.10.00298
MA0091.10.0157
MA0092.10.113
MA0093.10.0677
MA0099.20.00211
MA0100.10.919
MA0101.10.00315
MA0102.20.0248
MA0103.10.0658
MA0104.20.169
MA0105.10.483
MA0106.10.0651
MA0107.10.00599
MA0108.20.294
MA0111.10.976
MA0112.28.35297e-5
MA0113.10.404
MA0114.10.663
MA0115.10.652
MA0116.10.0073
MA0117.10.122
MA0119.10.124
MA0122.10.49
MA0124.10.371
MA0125.10.103
MA0131.10.257
MA0135.10.124
MA0136.11.16652e-10
MA0137.20.447
MA0138.20.0556
MA0139.10.976
MA0140.10.0393
MA0141.10.281
MA0142.10.189
MA0143.10.342
MA0144.10.671
MA0145.10.24
MA0146.10.283
MA0147.10.329
MA0148.10.599
MA0149.10.923
MA0150.10.00375
MA0152.10.0123
MA0153.10.999
MA0154.10.077
MA0155.10.27
MA0156.12.65531e-9
MA0157.10.761
MA0159.10.417
MA0160.10.35
MA0162.10.0503
MA0163.13.57348e-4
MA0164.10.988
MA0258.10.121
MA0259.10.332



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: CNhs12641

Novel motifP-value
10.426
100.343
1000.686
1010.266
1020.219
1030.218
1040.72
1050.0397
1060.54
1070.216
1080.176
1090.349
110.419
1100.179
1110.497
1120.277
1130.385
1140.0624
1150.0115
1160.029
1170.921
1180.472
1191
120.212
1200.234
1210.736
1220.122
1230.0149
1240.525
1250.917
1260.991
1270.521
1280.467
1290.731
130.5
1300.682
1310.201
1320.13
1330.54
1340.599
1350.707
1360.831
1370.894
1380.362
1390.361
140.265
1400.906
1410.656
1420.895
1430.907
1440.278
1450.696
1460.298
1470.178
1480.903
1490.00601
150.891
1500.333
1510.527
1520.153
1530.687
1540.716
1550.129
1560.571
1570.704
1580.0259
1590.725
160.0043
1600.215
1610.693
1620.642
1630.487
1640.152
1650.787
1660.0739
1670.823
1680.876
1690.011
170.295
180.264
190.0028
20.18
200.56
210.0412
220.15
230.223
240.304
250.72
260.306
270.471
280.19
290.243
30.342
300.443
310.462
323.57833e-19
330.753
340.658
350.942
360.0808
370.0878
380.991
390.11
40.732
400.895
410.554
420.899
430.301
440.0683
450.933
460.194
470.747
480.711
490.776
50.95
500.623
510.509
520.992
530.222
540.447
550.305
560.791
570.832
580.478
590.00754
60.334
600.831
610.998
620.626
630.232
640.905
650.241
660.272
670.776
680.269
690.113
70.389
700.1
710.193
720.567
730.1
740.143
750.481
760.977
770.00521
780.494
791.28636e-4
80.12
800.23
810.411
820.152
830.986
840.329
850.215
860.963
870.614
880.409
890.00843
90.35
900.288
910.504
920.239
930.136
940.268
950.395
960.843
970.742
980.812
990.00191



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: CNhs12641


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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