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FF:10066-101I3: 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 16:52, 29 March 2012


Name:skeletal muscle, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskeletal muscle
dev stage22 weeks fetus
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA503105
catalog numberCat:RtHFN: Skeletal musc
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-penis0.0408
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-0.136
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs11776

Jaspar motifP-value
MA0002.20.0132
MA0003.10.161
MA0004.10.106
MA0006.10.679
MA0007.10.266
MA0009.10.0876
MA0014.10.157
MA0017.10.625
MA0018.20.00649
MA0019.10.987
MA0024.10.177
MA0025.10.0151
MA0027.10.815
MA0028.17.18225e-8
MA0029.10.838
MA0030.10.0461
MA0031.10.00421
MA0035.20.492
MA0038.10.57
MA0039.20.00708
MA0040.10.8
MA0041.10.206
MA0042.10.806
MA0043.11.41417e-4
MA0046.10.0415
MA0047.20.0522
MA0048.10.0504
MA0050.11.16836e-4
MA0051.10.0013
MA0052.11.0344e-23
MA0055.14.9035e-4
MA0057.10.917
MA0058.10.0155
MA0059.10.0835
MA0060.10.00836
MA0061.11.1361e-4
MA0062.24.03688e-15
MA0065.20.972
MA0066.10.51
MA0067.10.0575
MA0068.10.0406
MA0069.10.458
MA0070.10.792
MA0071.10.159
MA0072.10.534
MA0073.10.408
MA0074.10.541
MA0076.11.03972e-9
MA0077.10.75
MA0078.10.534
MA0079.20.46
MA0080.25.96609e-8
MA0081.10.015
MA0083.10.00296
MA0084.10.596
MA0087.10.351
MA0088.10.393
MA0090.10.225
MA0091.14.34533e-5
MA0092.10.661
MA0093.10.0653
MA0099.21.08586e-18
MA0100.10.0944
MA0101.11.32945e-4
MA0102.29.56537e-4
MA0103.10.2
MA0104.20.00342
MA0105.10.00233
MA0106.10.00293
MA0107.12.16835e-4
MA0108.21.84918e-13
MA0111.10.581
MA0112.20.0119
MA0113.10.362
MA0114.10.797
MA0115.10.876
MA0116.10.0263
MA0117.10.0797
MA0119.10.258
MA0122.10.294
MA0124.10.347
MA0125.10.374
MA0131.10.173
MA0135.10.402
MA0136.12.289e-14
MA0137.20.0741
MA0138.20.147
MA0139.10.0873
MA0140.10.607
MA0141.10.408
MA0142.10.0182
MA0143.10.796
MA0144.10.285
MA0145.10.187
MA0146.10.802
MA0147.10.00755
MA0148.10.0399
MA0149.10.0559
MA0150.12.46564e-7
MA0152.10.0285
MA0153.10.799
MA0154.10.137
MA0155.10.0038
MA0156.11.57604e-16
MA0157.10.0116
MA0159.10.915
MA0160.10.117
MA0162.10.348
MA0163.10.752
MA0164.10.796
MA0258.10.00511
MA0259.10.275



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: CNhs11776

Novel motifP-value
10.895
100.19
1000.583
1010.375
1020.565
1030.271
1040.953
1050.883
1060.272
1070.0389
1080.073
1090.0451
110.637
1100.492
1110.698
1120.738
1131.02994e-5
1140.188
1150.0739
1160.0541
1170.0206
1180.0248
1190.214
120.981
1200.746
1210.152
1220.0153
1230.422
1240.0699
1250.389
1260.743
1270.39
1280.0819
1290.997
130.641
1300.662
1310.841
1320.0627
1330.476
1340.331
1350.237
1360.136
1370.86
1380.8
1390.148
140.512
1400.907
1410.434
1420.821
1430.00692
1440.166
1450.753
1460.405
1470.0449
1480.986
1490.128
150.178
1500.917
1510.568
1520.456
1530.189
1540.987
1550.352
1560.435
1570.41
1580.498
1590.795
160.473
1600.244
1610.478
1620.0718
1630.0175
1640.465
1650.416
1660.0337
1670.107
1680.766
1690.066
170.962
180.264
190.00693
20.138
200.0181
210.226
220.564
230.629
240.0562
250.533
260.602
270.958
280.219
290.215
30.439
300.175
310.355
324.31629e-9
330.255
340.121
350.823
360.124
370.224
380.854
390.401
40.358
400.634
410.549
420.225
430.899
440.0523
450.314
460.799
470.929
480.825
490.781
50.379
500.646
510.809
520.244
530.823
540.451
550.359
560.734
570.703
580.902
590.891
60.735
600.546
610.356
620.68
630.588
640.956
650.511
660.0718
670.388
680.0844
690.256
70.911
700.996
710.267
720.317
730.485
740.296
750.0545
760.174
770.343
780.509
790.047
80.425
800.68
810.632
820.306
830.371
840.495
850.107
860.444
870.00564
880.512
890.265
90.816
900.52
910.0664
920.911
930.717
940.195
950.0015
960.762
970.829
980.792
990.0154



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: CNhs11776


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

UBERON: Anatomy
0000061 (anatomical structure)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0009142 (entire embryonic mesenchyme)

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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