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FF:11363-117I4: 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 17:04, 29 March 2012


Name:Smooth Muscle Cells - Coronary Artery, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecoronary artery
dev stage51 years old adult
sexmale
age51
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 number1369
catalog numberCA350-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-0.0722
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-0.401
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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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: CNhs11987

Jaspar motifP-value
MA0002.20.226
MA0003.10.199
MA0004.10.667
MA0006.10.324
MA0007.10.146
MA0009.10.411
MA0014.10.981
MA0017.10.163
MA0018.20.00359
MA0019.10.936
MA0024.15.81734e-6
MA0025.10.122
MA0027.10.645
MA0028.10.33
MA0029.10.827
MA0030.10.125
MA0031.10.0321
MA0035.20.507
MA0038.10.0173
MA0039.20.599
MA0040.10.732
MA0041.10.232
MA0042.10.718
MA0043.10.00421
MA0046.10.52
MA0047.20.483
MA0048.10.533
MA0050.11.89805e-4
MA0051.10.0457
MA0052.10.958
MA0055.10.957
MA0057.10.0881
MA0058.10.553
MA0059.10.0832
MA0060.12.67747e-5
MA0061.10.466
MA0062.20.032
MA0065.20.0173
MA0066.10.0715
MA0067.10.217
MA0068.15.41447e-4
MA0069.10.434
MA0070.10.421
MA0071.10.202
MA0072.10.37
MA0073.10.565
MA0074.10.339
MA0076.10.126
MA0077.10.38
MA0078.10.215
MA0079.20.692
MA0080.29.47596e-5
MA0081.10.334
MA0083.10.146
MA0084.10.583
MA0087.10.937
MA0088.10.338
MA0090.10.0381
MA0091.10.0333
MA0092.10.095
MA0093.10.582
MA0099.22.46901e-4
MA0100.10.149
MA0101.10.437
MA0102.20.0393
MA0103.10.589
MA0104.20.975
MA0105.10.0665
MA0106.10.352
MA0107.10.687
MA0108.20.0514
MA0111.10.321
MA0112.29.37095e-4
MA0113.10.433
MA0114.10.212
MA0115.10.691
MA0116.10.0301
MA0117.10.722
MA0119.10.00347
MA0122.10.402
MA0124.10.974
MA0125.10.372
MA0131.10.336
MA0135.10.682
MA0136.10.00116
MA0137.20.0597
MA0138.20.0565
MA0139.10.39
MA0140.10.559
MA0141.10.039
MA0142.10.161
MA0143.10.834
MA0144.10.733
MA0145.10.0699
MA0146.10.184
MA0147.10.612
MA0148.10.227
MA0149.10.112
MA0150.10.26
MA0152.10.879
MA0153.10.81
MA0154.10.07
MA0155.10.112
MA0156.10.0625
MA0157.10.504
MA0159.10.0218
MA0160.10.219
MA0162.10.0709
MA0163.17.15597e-5
MA0164.10.517
MA0258.10.00555
MA0259.10.726



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: CNhs11987

Novel motifP-value
10.104
100.801
1000.891
1010.704
1020.765
1030.161
1040.364
1050.966
1060.011
1070.0524
1080.304
1090.0987
110.0452
1100.305
1110.878
1120.259
1130.225
1140.0296
1150.299
1160.149
1170.313
1180.585
1190.167
120.912
1200.242
1210.648
1221
1230.909
1240.891
1250.116
1260.709
1270.0459
1280.0695
1290.575
130.536
1300.512
1310.161
1320.87
1330.756
1340.841
1350.413
1360.953
1370.926
1380.384
1390.0126
140.873
1400.69
1410.35
1420.708
1430.00346
1440.936
1450.2
1460.353
1470.159
1480.501
1490.056
150.0912
1500.341
1510.288
1520.0354
1530.973
1540.803
1550.543
1560.618
1570.76
1580.346
1590.533
160.0904
1600.0393
1610.308
1620.81
1630.596
1640.231
1650.707
1660.667
1670.366
1680.778
1690.0226
170.22
180.0636
190.0863
20.534
200.621
210.475
220.211
230.106
240.433
250.885
260.0308
270.442
280.467
290.261
30.229
300.847
310.419
322.49955e-4
330.824
340.639
350.301
360.847
370.0537
380.485
390.33
40.453
400.377
410.668
420.434
430.194
440.118
450.514
460.0437
470.121
480.118
490.299
50.495
500.606
510.469
520.623
530.813
540.618
550.174
560.387
570.163
580.942
590.0356
60.764
600.302
610.831
620.432
630.0726
640.164
650.101
660.84
670.227
680.16
690.0325
70.756
700.00631
710.173
720.904
730.0212
740.385
750.331
760.972
770.0203
780.325
790.0471
80.0124
800.919
810.228
820.25
830.344
840.618
850.0288
860.559
870.0828
880.0715
890.0502
90.555
900.669
910.254
920.23
930.806
940.0935
950.225
960.513
970.442
980.17
990.0493



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: CNhs11987


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)
0002592 (smooth muscle cell of the coronary artery)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000062 (organ)
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)
0000948 (heart)
0001009 (circulatory system)
0001015 (musculature)
0001048 (primordium)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001621 (coronary artery)
0001637 (artery)
0001981 (blood vessel)
0002036 (striated muscle tissue)
0002049 (vasculature)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003081 (lateral plate mesoderm)
0003082 (myotome)
0003084 (heart primordium)
0003104 (mesenchyme)
0003498 (heart blood vessel)
0003509 (arterial blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004290 (dermomyotome)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004571 (systemic arterial system)
0004572 (arterial system)
0004573 (systemic artery)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0005985 (coronary vessel)
0006965 (vascular cord)
0007005 (cardiac mesoderm)
0007100 (primary circulatory organ)
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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