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FF:11286-116I8: 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 16:39, 29 March 2012


Name:Smooth Muscle Cells - Coronary Artery, donor1
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 stage41 years old adult
sexfemale
age41
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 number1346
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-0.163
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-0.186
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
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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: CNhs11088

Jaspar motifP-value
MA0002.20.288
MA0003.10.234
MA0004.10.967
MA0006.10.186
MA0007.10.205
MA0009.10.386
MA0014.10.977
MA0017.10.439
MA0018.29.63559e-4
MA0019.10.468
MA0024.11.03643e-5
MA0025.10.9
MA0027.10.766
MA0028.10.677
MA0029.10.209
MA0030.10.213
MA0031.10.0269
MA0035.20.409
MA0038.10.602
MA0039.20.364
MA0040.10.484
MA0041.10.308
MA0042.10.786
MA0043.10.00623
MA0046.10.458
MA0047.20.651
MA0048.10.57
MA0050.18.42175e-5
MA0051.10.265
MA0052.10.631
MA0055.10.46
MA0057.10.0968
MA0058.10.885
MA0059.10.208
MA0060.10.106
MA0061.10.509
MA0062.20.36
MA0065.20.626
MA0066.10.3
MA0067.10.0232
MA0068.10.791
MA0069.10.939
MA0070.10.543
MA0071.10.666
MA0072.10.615
MA0073.10.677
MA0074.10.584
MA0076.10.595
MA0077.10.136
MA0078.10.177
MA0079.20.258
MA0080.20.0589
MA0081.10.765
MA0083.17.89274e-6
MA0084.10.823
MA0087.10.673
MA0088.10.407
MA0090.10.00109
MA0091.10.111
MA0092.10.102
MA0093.10.893
MA0099.26.34839e-17
MA0100.10.075
MA0101.10.8
MA0102.20.0461
MA0103.10.268
MA0104.20.414
MA0105.10.569
MA0106.10.206
MA0107.10.367
MA0108.22.71274e-8
MA0111.10.0587
MA0112.20.049
MA0113.10.087
MA0114.10.695
MA0115.10.793
MA0116.10.356
MA0117.10.278
MA0119.10.0568
MA0122.10.692
MA0124.10.448
MA0125.10.981
MA0131.10.436
MA0135.10.793
MA0136.10.347
MA0137.20.32
MA0138.20.893
MA0139.10.772
MA0140.10.226
MA0141.10.418
MA0142.10.716
MA0143.10.521
MA0144.10.512
MA0145.10.102
MA0146.10.247
MA0147.10.899
MA0148.10.704
MA0149.10.631
MA0150.10.0455
MA0152.10.398
MA0153.10.423
MA0154.10.194
MA0155.10.0373
MA0156.10.682
MA0157.10.298
MA0159.10.231
MA0160.10.569
MA0162.10.0995
MA0163.10.202
MA0164.10.632
MA0258.10.279
MA0259.10.661



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: CNhs11088

Novel motifP-value
10.905
100.144
1000.9
1010.637
1020.95
1030.524
1040.339
1050.378
1060.0454
1070.0273
1080.608
1090.0876
110.101
1100.504
1110.448
1120.624
1130.215
1140.314
1150.688
1160.0643
1170.799
1180.697
1190.34
120.697
1200.203
1210.421
1220.428
1230.0341
1240.961
1250.69
1260.902
1270.732
1280.204
1290.601
130.985
1300.245
1310.137
1320.409
1330.911
1340.15
1350.246
1360.852
1370.297
1380.494
1390.32
140.553
1400.585
1410.42
1420.941
1430.0365
1440.999
1450.17
1460.363
1470.192
1480.914
1490.153
150.684
1500.128
1510.482
1520.00846
1530.396
1540.25
1550.0162
1560.96
1570.833
1580.0311
1590.286
160.249
1600.0936
1610.567
1620.755
1630.941
1640.856
1650.559
1660.753
1670.466
1680.478
1690.0682
170.103
180.12
190.159
20.397
200.353
210.584
220.142
230.145
240.198
250.272
260.264
270.484
280.227
290.861
30.519
300.118
310.52
320.0451
330.846
340.201
350.924
360.781
370.154
380.541
390.255
40.744
400.159
410.795
420.649
430.387
440.829
450.172
460.257
470.406
480.18
490.683
50.766
500.395
510.773
520.554
530.609
540.502
550.259
560.511
570.588
580.548
590.0937
60.741
600.592
610.938
620.706
630.274
640.503
650.144
660.391
670.996
680.291
690.359
70.813
700.279
710.304
720.825
730.0037
740.699
750.563
760.346
770.00375
780.603
790.337
80.0866
800.303
810.806
820.639
830.988
840.97
850.149
860.879
870.0275
880.182
890.0659
90.149
900.136
910.46
920.569
930.903
940.769
950.111
960.898
970.25
980.856
990.00571



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: CNhs11088


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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