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FF:11433-118H2: 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 - Brachiocephalic, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrachiocephalic artery
dev stageNA
sexunknown
ageNA
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 number1851
catalog numbercustom
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-0.192
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-0.139
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: CNhs12043

Jaspar motifP-value
MA0002.20.175
MA0003.10.529
MA0004.10.00158
MA0006.10.209
MA0007.10.838
MA0009.10.157
MA0014.10.787
MA0017.10.505
MA0018.20.00746
MA0019.10.412
MA0024.12.27224e-4
MA0025.10.953
MA0027.10.901
MA0028.14.26692e-5
MA0029.10.224
MA0030.10.891
MA0031.10.0595
MA0035.20.563
MA0038.10.385
MA0039.20.615
MA0040.10.557
MA0041.10.164
MA0042.10.657
MA0043.10.746
MA0046.10.407
MA0047.20.576
MA0048.10.302
MA0050.11.80983e-4
MA0051.10.581
MA0052.10.633
MA0055.10.341
MA0057.10.21
MA0058.14.78128e-4
MA0059.10.701
MA0060.15.87434e-4
MA0061.10.28
MA0062.20.0132
MA0065.20.0974
MA0066.10.978
MA0067.10.0194
MA0068.10.595
MA0069.10.919
MA0070.10.0909
MA0071.10.937
MA0072.10.937
MA0073.10.325
MA0074.10.686
MA0076.17.75504e-5
MA0077.10.238
MA0078.10.223
MA0079.20.113
MA0080.22.8319e-5
MA0081.10.406
MA0083.14.80087e-4
MA0084.10.0485
MA0087.10.298
MA0088.10.499
MA0090.15.03149e-5
MA0091.10.574
MA0092.10.0373
MA0093.10.00917
MA0099.23.14263e-10
MA0100.10.132
MA0101.10.698
MA0102.20.291
MA0103.11.63101e-4
MA0104.20.0187
MA0105.10.036
MA0106.10.0394
MA0107.10.544
MA0108.20.00426
MA0111.10.00687
MA0112.20.433
MA0113.10.918
MA0114.10.304
MA0115.10.49
MA0116.10.0413
MA0117.10.921
MA0119.10.426
MA0122.10.583
MA0124.10.349
MA0125.10.767
MA0131.10.641
MA0135.10.661
MA0136.10.033
MA0137.20.164
MA0138.20.45
MA0139.10.793
MA0140.10.531
MA0141.10.696
MA0142.10.622
MA0143.10.692
MA0144.10.11
MA0145.10.449
MA0146.10.332
MA0147.10.236
MA0148.10.281
MA0149.10.755
MA0150.10.364
MA0152.10.153
MA0153.10.489
MA0154.10.215
MA0155.10.927
MA0156.10.463
MA0157.10.465
MA0159.10.606
MA0160.10.475
MA0162.10.0511
MA0163.10.927
MA0164.10.96
MA0258.10.102
MA0259.10.246



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: CNhs12043

Novel motifP-value
10.49
100.225
1000.023
1010.091
1020.649
1030.392
1040.581
1050.258
1060.37
1070.684
1080.599
1090.852
110.826
1100.723
1110.115
1120.762
1130.143
1140.711
1150.683
1160.131
1170.603
1180.801
1190.91
120.877
1200.288
1210.994
1220.655
1230.0199
1240.0708
1250.808
1260.365
1270.463
1280.386
1290.579
130.171
1300.86
1310.021
1320.617
1330.288
1340.18
1350.414
1360.169
1370.453
1380.897
1390.0252
140.0848
1400.667
1410.629
1420.816
1430.324
1440.509
1450.582
1460.405
1470.201
1480.252
1490.475
150.511
1500.535
1510.885
1520.0157
1530.708
1540.928
1550.00184
1560.569
1570.509
1580.0165
1590.233
160.346
1600.449
1610.798
1620.611
1630.413
1640.203
1650.115
1660.0444
1670.953
1680.831
1690.812
170.66
180.0928
190.913
20.646
200.684
210.754
220.891
230.126
240.604
250.661
260.441
270.427
280.553
290.387
30.882
300.239
310.976
320.00542
330.0912
340.839
350.521
360.0441
370.202
380.533
390.471
40.454
400.107
410.591
420.65
430.397
440.673
450.954
460.75
470.876
480.704
490.0349
50.963
500.834
510.304
520.435
530.199
540.964
550.423
560.36
570.846
580.529
590.817
60.276
600.337
610.281
620.805
630.82
640.783
650.958
660.971
670.459
680.636
690.745
70.899
700.528
710.48
720.138
730.00343
740.633
750.652
760.71
770.0655
780.279
790.813
80.878
800.576
810.251
820.439
830.42
840.837
850.806
860.16
870.00162
880.813
890.325
90.937
900.979
910.32
920.771
930.966
940.889
950.22
960.208
970.517
980.0264
990.0554



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: CNhs12043


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)
0002589 (smooth muscle cell of the brachiocephalic vasculature)

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)
0001009 (circulatory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001529 (brachiocephalic 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)
0003104 (mesenchyme)
0003509 (arterial blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
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)
0006965 (vascular cord)
0007204 (brachiocephalic vasculature)
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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