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FF:12652-134H6: 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_rep1 (LK31)
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-penis0.0679
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-0.26
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: CNhs13349

Jaspar motifP-value
MA0002.20.523
MA0003.10.406
MA0004.10.624
MA0006.10.295
MA0007.10.323
MA0009.10.777
MA0014.10.966
MA0017.10.632
MA0018.22.27702e-5
MA0019.10.964
MA0024.14.00198e-6
MA0025.10.00204
MA0027.10.814
MA0028.10.578
MA0029.10.984
MA0030.10.0801
MA0031.10.157
MA0035.20.0852
MA0038.10.00193
MA0039.20.0527
MA0040.10.381
MA0041.10.61
MA0042.10.897
MA0043.11.52323e-4
MA0046.10.0555
MA0047.20.33
MA0048.10.233
MA0050.16.61446e-5
MA0051.10.0754
MA0052.10.05
MA0055.10.306
MA0057.10.42
MA0058.10.47
MA0059.10.129
MA0060.15.26532e-11
MA0061.10.151
MA0062.20.00876
MA0065.20.171
MA0066.10.073
MA0067.10.00329
MA0068.10.235
MA0069.10.418
MA0070.10.634
MA0071.10.721
MA0072.10.849
MA0073.10.879
MA0074.10.18
MA0076.10.124
MA0077.10.251
MA0078.10.214
MA0079.20.0589
MA0080.28.55821e-6
MA0081.10.136
MA0083.10.00746
MA0084.10.282
MA0087.10.393
MA0088.10.402
MA0090.10.184
MA0091.10.107
MA0092.10.118
MA0093.10.568
MA0099.20.00444
MA0100.10.189
MA0101.10.753
MA0102.20.145
MA0103.10.826
MA0104.20.752
MA0105.11.79712e-4
MA0106.11.96428e-4
MA0107.10.791
MA0108.20.985
MA0111.10.922
MA0112.20.00331
MA0113.10.516
MA0114.10.679
MA0115.10.194
MA0116.10.021
MA0117.10.58
MA0119.10.0343
MA0122.10.731
MA0124.10.385
MA0125.10.213
MA0131.10.131
MA0135.10.261
MA0136.13.16353e-4
MA0137.20.0974
MA0138.20.227
MA0139.10.208
MA0140.10.527
MA0141.10.273
MA0142.10.615
MA0143.10.241
MA0144.10.568
MA0145.10.224
MA0146.10.807
MA0147.10.84
MA0148.10.839
MA0149.10.154
MA0150.10.755
MA0152.10.0449
MA0153.10.295
MA0154.10.0312
MA0155.10.307
MA0156.10.0238
MA0157.10.614
MA0159.10.145
MA0160.10.426
MA0162.10.0303
MA0163.11.55672e-6
MA0164.10.749
MA0258.10.106
MA0259.10.61



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: CNhs13349

Novel motifP-value
10.178
100.322
1000.304
1010.911
1020.849
1030.118
1040.874
1050.484
1060.0323
1070.125
1080.257
1090.202
110.0613
1100.126
1110.139
1120.211
1130.0622
1140.0151
1150.334
1160.0596
1170.182
1180.552
1190.195
120.818
1200.0343
1210.993
1220.114
1230.145
1240.975
1250.322
1260.432
1270.711
1280.113
1290.811
130.281
1300.586
1310.685
1320.985
1330.68
1340.773
1350.402
1360.964
1370.143
1380.877
1390.222
140.75
1400.107
1410.628
1420.879
1430.0308
1440.259
1450.288
1460.848
1470.196
1480.0409
1490.00802
150.442
1500.217
1510.666
1520.079
1530.723
1540.678
1550.109
1560.923
1570.182
1580.0308
1590.109
160.0546
1600.0425
1610.965
1620.136
1630.648
1640.0247
1650.916
1660.439
1670.486
1680.605
1690.0836
170.0786
180.0767
190.0541
20.576
200.954
210.451
220.576
230.163
240.775
250.554
260.228
270.253
280.345
290.158
30.117
300.905
310.514
323.88192e-5
330.375
340.652
350.0974
360.235
370.017
380.576
390.37
40.912
400.37
410.692
420.632
430.16
440.0502
450.741
460.0501
470.184
480.235
490.337
50.448
500.744
510.548
520.776
530.551
540.446
550.357
560.504
570.143
580.985
590.0408
60.63
600.388
610.617
620.274
630.223
640.799
650.144
660.78
670.284
680.805
690.43
70.933
700.0287
710.0888
720.512
730.0328
740.0581
750.235
760.375
770.0309
780.429
790.00318
80.019
800.568
810.245
820.0377
830.959
840.938
850.121
860.626
870.175
880.274
890.0332
90.481
900.0791
910.526
920.123
930.567
940.325
950.229
960.305
970.597
980.97
990.078



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: CNhs13349


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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