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FF:11365-117I6: 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 17:05, 29 March 2012


Name:Smooth Muscle Cells - Pulmonary 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
tissuepulmonary 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 numberCA352-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-0.00518
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-0.208
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: CNhs11989

Jaspar motifP-value
MA0002.20.716
MA0003.10.267
MA0004.10.648
MA0006.10.194
MA0007.10.114
MA0009.10.439
MA0014.10.862
MA0017.10.879
MA0018.24.69563e-6
MA0019.10.734
MA0024.10.00227
MA0025.10.027
MA0027.10.655
MA0028.18.51221e-5
MA0029.10.274
MA0030.10.0611
MA0031.10.0489
MA0035.20.368
MA0038.10.025
MA0039.20.357
MA0040.10.52
MA0041.10.474
MA0042.10.838
MA0043.11.54241e-5
MA0046.10.459
MA0047.20.735
MA0048.10.56
MA0050.10.827
MA0051.10.886
MA0052.10.531
MA0055.10.755
MA0057.10.0785
MA0058.10.344
MA0059.10.821
MA0060.13.50974e-4
MA0061.10.848
MA0062.21.01147e-10
MA0065.20.374
MA0066.10.766
MA0067.10.0367
MA0068.10.851
MA0069.10.758
MA0070.10.974
MA0071.10.528
MA0072.10.938
MA0073.10.967
MA0074.10.153
MA0076.11.12091e-5
MA0077.10.579
MA0078.10.361
MA0079.20.87
MA0080.22.42816e-7
MA0081.10.0058
MA0083.10.031
MA0084.10.415
MA0087.10.516
MA0088.10.509
MA0090.10.038
MA0091.10.0894
MA0092.10.119
MA0093.10.504
MA0099.20.0114
MA0100.10.0955
MA0101.10.155
MA0102.20.305
MA0103.10.502
MA0104.20.243
MA0105.10.326
MA0106.10.179
MA0107.10.392
MA0108.20.00613
MA0111.10.385
MA0112.20.00541
MA0113.10.325
MA0114.10.936
MA0115.10.974
MA0116.10.0915
MA0117.10.174
MA0119.10.153
MA0122.10.997
MA0124.10.225
MA0125.10.465
MA0131.10.076
MA0135.10.259
MA0136.14.31726e-11
MA0137.20.932
MA0138.20.537
MA0139.10.963
MA0140.10.252
MA0141.10.223
MA0142.10.525
MA0143.10.38
MA0144.10.502
MA0145.10.175
MA0146.10.174
MA0147.10.537
MA0148.10.451
MA0149.10.726
MA0150.10.959
MA0152.10.00814
MA0153.10.173
MA0154.10.181
MA0155.10.0664
MA0156.17.36409e-6
MA0157.10.977
MA0159.10.48
MA0160.10.83
MA0162.10.166
MA0163.10.0184
MA0164.10.705
MA0258.10.105
MA0259.10.497



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: CNhs11989

Novel motifP-value
10.665
100.868
1000.884
1010.824
1020.648
1030.294
1040.583
1050.918
1060.0229
1070.0165
1080.472
1090.272
110.159
1100.305
1110.647
1120.407
1130.115
1140.195
1150.203
1160.0462
1170.937
1180.739
1190.45
120.795
1200.755
1210.837
1220.218
1230.141
1240.6
1250.872
1260.597
1270.709
1280.0557
1290.974
130.416
1300.211
1310.626
1320.394
1330.399
1340.903
1350.357
1360.653
1370.615
1380.444
1390.263
140.728
1400.535
1410.472
1420.234
1430.268
1440.209
1450.0965
1460.182
1470.206
1480.892
1490.0527
150.998
1500.339
1510.479
1520.0534
1530.648
1540.756
1550.0331
1560.426
1570.621
1580.0145
1590.276
160.0582
1600.0747
1610.718
1620.151
1630.995
1640.501
1650.995
1660.469
1670.719
1680.488
1690.0433
170.184
180.0992
190.0571
20.162
200.264
210.33
220.121
230.104
240.775
250.168
260.0143
270.135
280.22
290.849
30.544
300.165
310.419
326.46538e-9
330.821
340.343
350.702
360.126
370.325
380.739
390.172
40.931
400.755
410.988
420.832
430.217
440.434
450.355
460.0904
470.667
480.303
490.372
50.688
500.455
510.323
520.53
530.467
540.4
550.0896
560.508
570.813
580.562
590.0282
60.826
600.405
610.409
620.846
630.236
640.507
650.139
660.401
670.652
680.155
690.401
70.513
700.00742
710.263
720.876
730.0827
740.562
750.7
760.608
770.0236
780.406
790.00497
80.0374
800.387
810.405
820.657
830.688
840.712
850.0224
860.825
870.212
880.183
890.0577
90.292
900.877
910.275
920.166
930.943
940.822
950.623
960.771
970.493
980.766
990.00449



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: CNhs11989


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)
0002591 (smooth muscle cell of the pulmonary 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)
0001637 (artery)
0001981 (blood vessel)
0002012 (pulmonary artery)
0002036 (striated muscle tissue)
0002049 (vasculature)
0002050 (embryonic structure)
0002061 (truncus arteriosus)
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)
0003509 (arterial blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004145 (outflow tract)
0004290 (dermomyotome)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004572 (arterial system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0006965 (vascular cord)
0007005 (cardiac mesoderm)
0007100 (primary circulatory organ)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
0008886 (pulmonary 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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