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FF:11210-116A4: 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 16:33, 29 March 2012


Name:Smooth Muscle Cells - Aortic, donor0
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueaorta
dev stage54 years old adult
sexmale
age54
cell typesmooth muscle cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberCA354-R10a
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-penis-0.102
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-0.0236
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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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: CNhs10838

Jaspar motifP-value
MA0002.20.933
MA0003.10.513
MA0004.10.529
MA0006.10.131
MA0007.10.211
MA0009.10.528
MA0014.10.713
MA0017.10.446
MA0018.20.181
MA0019.10.347
MA0024.10.121
MA0025.10.733
MA0027.10.208
MA0028.10.29
MA0029.10.408
MA0030.10.665
MA0031.10.236
MA0035.20.768
MA0038.10.855
MA0039.20.925
MA0040.10.536
MA0041.10.389
MA0042.10.608
MA0043.10.232
MA0046.10.374
MA0047.20.753
MA0048.10.0866
MA0050.12.46633e-4
MA0051.10.168
MA0052.10.593
MA0055.10.0086
MA0057.10.731
MA0058.10.373
MA0059.10.965
MA0060.10.466
MA0061.10.916
MA0062.20.81
MA0065.20.0964
MA0066.10.928
MA0067.10.0934
MA0068.10.976
MA0069.10.426
MA0070.10.572
MA0071.10.508
MA0072.10.683
MA0073.10.992
MA0074.10.685
MA0076.10.167
MA0077.10.581
MA0078.10.434
MA0079.20.225
MA0080.20.00153
MA0081.10.425
MA0083.14.44978e-4
MA0084.10.227
MA0087.10.514
MA0088.10.436
MA0090.10.00533
MA0091.10.4
MA0092.10.317
MA0093.10.664
MA0099.27.40532e-16
MA0100.10.0965
MA0101.10.314
MA0102.20.968
MA0103.17.96857e-4
MA0104.20.0277
MA0105.10.453
MA0106.10.312
MA0107.10.516
MA0108.29.01263e-8
MA0111.12.55525e-4
MA0112.20.888
MA0113.10.539
MA0114.10.179
MA0115.10.805
MA0116.10.215
MA0117.10.954
MA0119.10.274
MA0122.10.76
MA0124.10.301
MA0125.10.55
MA0131.10.53
MA0135.10.776
MA0136.10.172
MA0137.20.858
MA0138.20.432
MA0139.10.828
MA0140.10.984
MA0141.10.764
MA0142.10.61
MA0143.10.699
MA0144.10.641
MA0145.10.294
MA0146.10.471
MA0147.10.133
MA0148.10.811
MA0149.10.913
MA0150.10.0352
MA0152.10.443
MA0153.10.777
MA0154.10.803
MA0155.10.0924
MA0156.10.513
MA0157.10.386
MA0159.10.332
MA0160.10.766
MA0162.10.133
MA0163.10.748
MA0164.10.496
MA0258.10.46
MA0259.10.463



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: CNhs10838

Novel motifP-value
10.765
100.192
1000.508
1010.0308
1020.494
1030.785
1040.477
1050.484
1060.439
1070.519
1080.428
1090.432
110.619
1100.898
1110.0789
1120.347
1130.0195
1140.555
1150.966
1160.0984
1170.408
1180.376
1190.99
120.208
1200.977
1210.507
1220.584
1230.0457
1240.421
1250.811
1260.672
1270.951
1280.822
1290.862
130.113
1300.0456
1310.374
1320.85
1330.229
1340.123
1350.166
1360.387
1370.932
1380.216
1390.94
140.369
1400.0801
1410.00707
1420.833
1430.0612
1440.627
1450.214
1460.397
1470.29
1480.219
1490.545
150.866
1500.304
1510.991
1520.00507
1530.503
1540.547
1550.0587
1560.761
1570.555
1580.0566
1590.41
160.985
1600.83
1610.163
1620.315
1630.568
1640.987
1650.878
1660.238
1670.296
1680.888
1690.316
170.673
180.43
190.906
20.403
200.355
210.511
220.325
230.242
240.103
250.0746
260.219
270.793
280.179
290.425
30.765
300.171
310.91
320.304
330.663
340.409
350.534
360.196
370.922
380.982
390.252
40.983
400.745
410.517
420.973
430.729
440.302
450.589
460.975
470.525
480.934
490.195
50.732
500.178
510.951
520.971
530.124
540.981
550.244
560.796
570.656
580.108
590.35
60.24
600.5
610.364
620.0747
630.44
640.658
650.635
660.366
670.865
680.295
690.397
70.336
700.983
710.913
720.579
730.00492
740.968
750.82
760.926
770.0879
780.121
790.765
80.598
800.929
810.789
820.146
830.717
840.776
850.889
860.694
870.0243
880.176
890.569
90.385
900.746
910.805
920.901
930.793
940.915
950.53
960.556
970.269
980.337
990.00496



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: CNhs10838


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)
0000056 (myoblast)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000359 (vascular associated smooth muscle cell)
0000393 (electrically responsive cell)
0000514 (smooth muscle myoblast)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002539 (aortic smooth muscle cell)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000947 (aorta)
0001009 (circulatory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001135 (smooth muscle tissue)
0001637 (artery)
0001981 (blood vessel)
0002036 (striated muscle tissue)
0002049 (vasculature)
0002050 (embryonic structure)
0002111 (artery smooth muscle tissue)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003081 (lateral plate mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0003509 (arterial blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004178 (aorta smooth muscle tissue)
0004237 (blood vessel smooth muscle)
0004290 (dermomyotome)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004571 (systemic arterial system)
0004572 (arterial system)
0004573 (systemic artery)
0004695 (arterial system smooth muscle)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006965 (vascular cord)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
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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