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{{f5samples
{{f5samples
|id=FF:10282-104F3
|F5samples=
|name=skeletal muscle - soleus muscle, donor1
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|sample_experimental_condition=
|sample_disease=
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|fonse_cell_line_closure=
Line 66: Line 34:
|fonse_treatment=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10282-104F3
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|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0011173
|name=skeletal muscle - soleus muscle, donor1
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs13454,LSID1024,release012,COMPLETED
|profile_rnaseq=,,,
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|rna_lot_number=1-Sm2
|rna_od260/230=1.79
|rna_od260/280=2.13
|rna_position=F3
|rna_rin=7.9
|rna_sample_type=total RNA
|rna_tube_id=104F3
|rna_weight_ug=18.53442
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=Alessandro Bonetti
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10282
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=skeletal muscle - soleus muscle
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}}
}}

Revision as of 14:05, 21 March 2012


Name:skeletal muscle - soleus muscle, 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 - soleus muscle
dev stageNA
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationAlessandro Bonetti
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1-Sm2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





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
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C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left1.374
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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: CNhs13454

Jaspar motifP-value
MA0002.20.0851
MA0003.10.9
MA0004.10.699
MA0006.10.864
MA0007.10.255
MA0009.10.607
MA0014.10.339
MA0017.10.0786
MA0018.20.0116
MA0019.10.372
MA0024.10.00214
MA0025.10.0216
MA0027.10.908
MA0028.15.65139e-4
MA0029.10.995
MA0030.10.82
MA0031.10.719
MA0035.20.387
MA0038.19.94579e-6
MA0039.20.00101
MA0040.10.848
MA0041.10.833
MA0042.10.883
MA0043.10.00142
MA0046.10.0161
MA0047.20.84
MA0048.10.0269
MA0050.11.51867e-5
MA0051.14.30918e-4
MA0052.15.78123e-17
MA0055.10.0326
MA0057.10.558
MA0058.10.565
MA0059.10.699
MA0060.11.74057e-9
MA0061.10.0663
MA0062.23.98843e-11
MA0065.20.00906
MA0066.10.263
MA0067.10.458
MA0068.10.0459
MA0069.10.169
MA0070.10.222
MA0071.10.183
MA0072.10.755
MA0073.10.939
MA0074.10.832
MA0076.12.86301e-5
MA0077.10.0343
MA0078.10.844
MA0079.20.0306
MA0080.23.3953e-8
MA0081.10.0103
MA0083.10.308
MA0084.10.947
MA0087.10.56
MA0088.10.91
MA0090.10.916
MA0091.10.0416
MA0092.10.117
MA0093.10.555
MA0099.21.47185e-7
MA0100.10.0991
MA0101.10.00844
MA0102.20.011
MA0103.10.33
MA0104.20.903
MA0105.10.256
MA0106.10.993
MA0107.10.00125
MA0108.20.05
MA0111.10.333
MA0112.21.07198e-7
MA0113.15.55031e-4
MA0114.10.0495
MA0115.10.0194
MA0116.10.0834
MA0117.10.925
MA0119.10.00692
MA0122.10.734
MA0124.10.612
MA0125.10.124
MA0131.10.211
MA0135.10.591
MA0136.11.71467e-9
MA0137.28.38516e-4
MA0138.20.782
MA0139.10.548
MA0140.10.334
MA0141.17.54283e-4
MA0142.10.355
MA0143.10.694
MA0144.10.0454
MA0145.10.0388
MA0146.10.786
MA0147.10.885
MA0148.10.454
MA0149.10.55
MA0150.10.513
MA0152.10.891
MA0153.10.925
MA0154.10.468
MA0155.10.607
MA0156.11.32898e-10
MA0157.10.551
MA0159.10.0376
MA0160.10.0158
MA0162.10.28
MA0163.10.00354
MA0164.10.278
MA0258.11.32355e-4
MA0259.10.832



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: CNhs13454

Novel motifP-value
10.0131
100.198
1000.737
1010.0609
1020.758
1030.629
1040.643
1050.498
1060.123
1070.0879
1080.0978
1090.535
110.131
1100.603
1110.00694
1120.198
1130.493
1140.0214
1150.225
1160.23
1170.68
1180.413
1190.0255
120.851
1200.477
1210.5
1220.0455
1230.212
1240.296
1250.384
1260.37
1270.341
1280.0286
1290.84
130.16
1300.156
1310.386
1320.589
1330.013
1340.93
1350.362
1360.0247
1370.845
1380.593
1393.9637e-4
140.351
1400.0116
1410.176
1420.998
1430.245
1440.466
1450.869
1460.918
1470.00219
1480.0748
1490.146
150.319
1500.752
1510.0878
1520.482
1530.117
1540.562
1550.296
1560.377
1570.268
1580.322
1590.151
160.333
1600.28
1610.816
1620.892
1630.463
1640.982
1654.95676e-4
1660.741
1670.0972
1680.638
1690.0209
170.364
180.323
190.0721
20.634
200.57
210.145
220.262
230.264
240.313
250.53
260.939
270.71
280.992
290.735
30.204
300.864
310.404
320.716
330.586
340.841
350.0428
360.623
370.0923
380.502
390.223
40.766
400.357
410.603
420.871
430.338
440.00258
450.728
460.0955
470.562
480.935
490.152
50.442
500.647
510.688
520.282
530.787
540.522
550.822
560.84
570.243
580.227
590.926
60.418
600.113
610.718
620.0419
630.0773
640.705
650.19
660.0631
670.901
680.566
690.218
70.246
700.0527
710.443
720.414
730.72
740.801
750.295
760.702
770.179
780.0259
790.0164
80.105
800.137
810.43
820.111
830.562
840.192
850.00687
860.359
870.0303
880.736
890.239
90.529
900.268
910.162
920.0737
930.8
940.643
950.0585
960.095
970.541
980.0038
990.747



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: CNhs13454


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
0000026 (appendage)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000154 (posterior region of body)
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)
0000978 (leg)
0001015 (musculature)
0001048 (primordium)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001383 (muscle of leg)
0001389 (soleus muscle)
0001630 (muscle organ)
0001665 (triceps surae)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002101 (limb)
0002103 (hindlimb)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002471 (zeugopod)
0002529 (limb segment)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003081 (lateral plate mesoderm)
0003082 (myotome)
0003102 (surface structure)
0003104 (mesenchyme)
0003661 (limb muscle)
0003663 (hindlimb muscle)
0003823 (hindlimb zeugopod)
0004120 (mesoderm-derived structure)
0004256 (hindlimb zeugopod muscle)
0004290 (dermomyotome)
0004347 (limb bud)
0004357 (paired limb/fin bud)
0004708 (paired limb/fin)
0004709 (pelvic appendage)
0005090 (muscle structure)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005732 (limb/fin field)
0005733 (limb field)
0006058 (multi-limb segment region)
0007023 (adult organism)
0008784 (lower limb segment)
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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