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FF:11435-118H4: 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 17:08, 29 March 2012


Name:Smooth Muscle Cells - Coronary Artery, donor3
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 stage39 years old adult
sexmale
age39
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 number1401
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-0.156
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-0.0424
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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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: CNhs12045

Jaspar motifP-value
MA0002.20.975
MA0003.10.247
MA0004.10.761
MA0006.10.183
MA0007.10.224
MA0009.10.834
MA0014.10.808
MA0017.10.554
MA0018.20.00127
MA0019.10.244
MA0024.10.00279
MA0025.10.4
MA0027.10.783
MA0028.10.316
MA0029.10.312
MA0030.10.0443
MA0031.10.00303
MA0035.20.935
MA0038.10.12
MA0039.20.886
MA0040.10.358
MA0041.10.288
MA0042.10.871
MA0043.10.0581
MA0046.10.962
MA0047.20.523
MA0048.10.488
MA0050.11.23608e-5
MA0051.10.0351
MA0052.10.0466
MA0055.10.118
MA0057.10.496
MA0058.10.427
MA0059.10.445
MA0060.10.00327
MA0061.10.437
MA0062.20.941
MA0065.20.32
MA0066.10.338
MA0067.10.0205
MA0068.10.904
MA0069.10.528
MA0070.10.763
MA0071.10.568
MA0072.10.551
MA0073.10.693
MA0074.10.0922
MA0076.10.66
MA0077.10.198
MA0078.10.0644
MA0079.20.492
MA0080.20.00101
MA0081.10.5
MA0083.10.024
MA0084.10.181
MA0087.10.31
MA0088.10.41
MA0090.10.0185
MA0091.10.108
MA0092.10.101
MA0093.10.787
MA0099.24.76626e-7
MA0100.10.148
MA0101.10.441
MA0102.20.2
MA0103.10.163
MA0104.20.384
MA0105.10.366
MA0106.10.0295
MA0107.10.435
MA0108.20.0235
MA0111.10.0716
MA0112.20.0363
MA0113.10.27
MA0114.10.737
MA0115.10.424
MA0116.10.836
MA0117.10.315
MA0119.10.293
MA0122.10.969
MA0124.10.256
MA0125.10.245
MA0131.10.348
MA0135.10.938
MA0136.10.00739
MA0137.20.227
MA0138.20.878
MA0139.10.967
MA0140.10.83
MA0141.10.164
MA0142.10.362
MA0143.10.673
MA0144.10.893
MA0145.10.161
MA0146.10.34
MA0147.10.703
MA0148.10.605
MA0149.10.798
MA0150.10.323
MA0152.10.243
MA0153.10.667
MA0154.10.292
MA0155.10.0193
MA0156.10.696
MA0157.10.109
MA0159.10.414
MA0160.10.945
MA0162.10.0118
MA0163.10.0503
MA0164.10.586
MA0258.10.222
MA0259.10.504



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: CNhs12045

Novel motifP-value
10.833
100.211
1000.816
1010.197
1020.987
1030.143
1040.515
1050.487
1060.351
1070.0804
1080.28
1090.0696
110.116
1100.21
1110.339
1120.783
1130.0256
1140.536
1150.0817
1160.039
1170.807
1180.714
1190.159
120.905
1200.0329
1210.959
1220.97
1230.0186
1240.334
1250.709
1260.699
1270.719
1280.283
1290.704
130.648
1300.239
1310.791
1320.867
1330.417
1340.238
1350.11
1360.152
1370.632
1380.511
1390.397
140.755
1400.668
1410.713
1420.426
1430.00959
1440.903
1450.417
1460.421
1470.184
1480.615
1490.113
150.687
1500.134
1510.634
1520.00995
1530.249
1540.418
1550.117
1560.962
1570.407
1580.0542
1590.486
160.123
1600.309
1610.55
1620.902
1630.947
1640.473
1650.534
1660.999
1670.618
1680.976
1690.0828
170.128
180.0717
190.227
20.0874
200.365
210.967
220.192
230.12
240.279
250.388
260.214
270.454
280.267
290.481
30.58
300.216
310.587
322.0821e-5
330.891
340.194
350.842
360.289
370.095
380.653
390.552
40.825
400.541
410.283
420.98
430.517
440.161
450.297
460.258
470.588
480.38
490.97
50.924
500.607
510.73
520.901
530.367
540.686
550.325
560.886
570.942
580.4
590.0554
60.989
600.851
610.923
620.898
630.482
640.7
650.0655
660.856
670.429
680.383
690.647
70.879
700.658
710.878
720.728
730.00118
740.56
750.681
760.58
775.83809e-4
780.685
790.146
80.0824
800.875
810.852
820.762
830.927
840.804
850.246
860.599
870.00267
880.712
890.00258
90.246
900.619
910.832
920.307
930.0656
940.592
950.0241
960.653
970.41
980.715
990.0124



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: CNhs12045


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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