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FF:12750-136A5: 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 17:31, 29 March 2012


Name:Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueaorta
dev stageNA
sexNA
ageNA
cell typesmooth muscle cell, vascular associated
cell lineNA
companyNA
collaborationLevon Khachigian (University of New South Wales)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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-penis0.173
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-0.325
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: CNhs13369

Jaspar motifP-value
MA0002.20.933
MA0003.10.545
MA0004.10.54
MA0006.10.14
MA0007.10.739
MA0009.10.724
MA0014.10.955
MA0017.10.483
MA0018.21.43274e-6
MA0019.10.806
MA0024.13.52368e-6
MA0025.15.40684e-4
MA0027.10.917
MA0028.10.182
MA0029.10.501
MA0030.10.0942
MA0031.10.444
MA0035.20.164
MA0038.17.85364e-4
MA0039.20.0223
MA0040.10.496
MA0041.10.868
MA0042.10.804
MA0043.11.46873e-6
MA0046.10.166
MA0047.20.719
MA0048.10.321
MA0050.12.65406e-4
MA0051.10.0362
MA0052.10.03
MA0055.10.772
MA0057.10.332
MA0058.10.319
MA0059.10.302
MA0060.13.31689e-13
MA0061.10.198
MA0062.22.18724e-4
MA0065.20.381
MA0066.10.0365
MA0067.10.00103
MA0068.10.823
MA0069.10.354
MA0070.10.641
MA0071.10.972
MA0072.10.932
MA0073.10.83
MA0074.10.216
MA0076.10.0225
MA0077.10.165
MA0078.10.124
MA0079.20.0757
MA0080.21.43234e-5
MA0081.10.0337
MA0083.10.048
MA0084.10.19
MA0087.10.793
MA0088.10.381
MA0090.10.151
MA0091.10.134
MA0092.10.181
MA0093.10.444
MA0099.20.145
MA0100.10.351
MA0101.10.903
MA0102.20.163
MA0103.10.448
MA0104.20.293
MA0105.16.32179e-4
MA0106.12.22003e-4
MA0107.10.865
MA0108.20.664
MA0111.10.741
MA0112.20.00283
MA0113.10.597
MA0114.10.806
MA0115.10.608
MA0116.10.0317
MA0117.10.715
MA0119.10.0385
MA0122.10.931
MA0124.10.959
MA0125.10.0617
MA0131.10.238
MA0135.10.0342
MA0136.13.86975e-5
MA0137.20.0268
MA0138.20.186
MA0139.10.27
MA0140.10.333
MA0141.10.451
MA0142.10.951
MA0143.10.35
MA0144.10.629
MA0145.10.36
MA0146.10.815
MA0147.10.612
MA0148.10.912
MA0149.10.106
MA0150.10.706
MA0152.10.144
MA0153.10.209
MA0154.10.0777
MA0155.10.274
MA0156.10.0049
MA0157.10.99
MA0159.10.498
MA0160.10.389
MA0162.10.0308
MA0163.14.02076e-6
MA0164.10.738
MA0258.10.049
MA0259.10.186



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: CNhs13369

Novel motifP-value
10.202
100.552
1000.443
1010.898
1020.933
1030.227
1040.828
1050.311
1060.00551
1070.0842
1080.239
1090.229
110.0768
1100.21
1110.103
1120.182
1130.0826
1140.0206
1150.0895
1160.0311
1170.347
1180.339
1190.114
120.997
1200.0146
1210.766
1220.106
1230.253
1240.879
1250.323
1260.597
1270.982
1280.0435
1290.408
130.506
1300.313
1310.297
1320.813
1330.838
1340.52
1350.387
1360.667
1370.167
1380.931
1390.193
140.916
1400.218
1410.736
1420.623
1430.022
1440.302
1450.135
1460.836
1470.153
1480.0888
1490.0556
150.392
1500.119
1510.757
1520.0407
1530.618
1540.829
1550.0387
1560.661
1570.269
1580.0314
1590.161
160.094
1600.124
1610.912
1620.0844
1630.95
1640.0168
1650.74
1660.42
1670.546
1680.456
1690.0705
170.115
180.089
190.0458
20.535
200.79
210.297
220.501
230.129
240.942
250.33
260.0858
270.312
280.456
290.0932
30.234
300.901
310.306
321.27625e-4
330.655
340.854
350.157
360.868
370.0179
380.477
390.297
40.953
400.929
410.618
420.847
430.189
440.0143
450.548
460.0513
470.289
480.169
490.449
50.417
500.832
510.635
520.533
530.432
540.523
550.101
560.649
570.384
580.821
590.0679
60.428
600.387
610.426
620.429
630.191
640.576
650.124
660.548
670.475
680.383
690.787
70.738
700.0418
710.216
720.777
730.0193
740.0376
750.349
760.399
770.0167
780.556
790.00343
80.0179
800.273
810.291
820.0269
830.852
840.878
850.0513
860.647
870.136
880.16
890.141
90.422
900.178
910.168
920.17
930.486
940.33
950.243
960.709
970.65
980.768
990.00807



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: CNhs13369


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)
0002539 (aortic smooth muscle cell)

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)
0000947 (aorta)
0001009 (circulatory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001135 (smooth muscle tissue)
0001637 (artery)
0001981 (blood vessel)
0002036 (striated muscle tissue)
0002049 (vasculature)
0002050 (embryonic structure)
0002111 (artery smooth muscle tissue)
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)
0004178 (aorta smooth muscle tissue)
0004237 (blood vessel smooth muscle)
0004290 (dermomyotome)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004571 (systemic arterial system)
0004572 (arterial system)
0004573 (systemic artery)
0004695 (arterial system smooth muscle)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006965 (vascular cord)
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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