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FF:12740-135I4: 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 FGF2, 00hr00min, biol_rep2 (LK2)
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-penis0.0955
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-0.316
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: CNhs13358

Jaspar motifP-value
MA0002.20.638
MA0003.10.384
MA0004.10.429
MA0006.10.321
MA0007.10.343
MA0009.10.957
MA0014.10.902
MA0017.10.565
MA0018.22.02711e-5
MA0019.10.903
MA0024.12.4779e-6
MA0025.13.23981e-4
MA0027.10.806
MA0028.10.455
MA0029.10.631
MA0030.10.0148
MA0031.10.204
MA0035.20.158
MA0038.18.17626e-4
MA0039.20.0278
MA0040.10.428
MA0041.10.501
MA0042.10.708
MA0043.16.28585e-6
MA0046.10.0252
MA0047.20.522
MA0048.10.178
MA0050.11.07192e-4
MA0051.10.0468
MA0052.10.0166
MA0055.10.789
MA0057.10.843
MA0058.10.238
MA0059.10.18
MA0060.11.40777e-11
MA0061.10.118
MA0062.20.00171
MA0065.20.333
MA0066.10.0595
MA0067.10.00386
MA0068.10.229
MA0069.10.212
MA0070.10.46
MA0071.10.914
MA0072.10.47
MA0073.10.581
MA0074.10.166
MA0076.10.0554
MA0077.10.0563
MA0078.10.14
MA0079.20.0732
MA0080.26.29001e-5
MA0081.10.073
MA0083.10.0175
MA0084.10.477
MA0087.10.818
MA0088.10.419
MA0090.10.127
MA0091.10.111
MA0092.10.266
MA0093.10.358
MA0099.20.0191
MA0100.10.44
MA0101.10.711
MA0102.20.168
MA0103.10.555
MA0104.20.671
MA0105.19.06963e-5
MA0106.18.3817e-4
MA0107.10.777
MA0108.20.619
MA0111.10.785
MA0112.20.00263
MA0113.10.311
MA0114.10.883
MA0115.10.544
MA0116.10.02
MA0117.10.68
MA0119.10.0788
MA0122.10.832
MA0124.10.533
MA0125.10.33
MA0131.10.203
MA0135.10.0746
MA0136.11.29668e-4
MA0137.20.0448
MA0138.20.124
MA0139.10.208
MA0140.10.631
MA0141.10.346
MA0142.10.909
MA0143.10.167
MA0144.10.798
MA0145.10.315
MA0146.10.906
MA0147.10.996
MA0148.10.948
MA0149.10.152
MA0150.10.883
MA0152.10.0831
MA0153.10.173
MA0154.10.04
MA0155.10.413
MA0156.10.00554
MA0157.10.706
MA0159.10.16
MA0160.10.537
MA0162.10.0617
MA0163.11.22138e-6
MA0164.10.792
MA0258.10.0956
MA0259.10.404



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: CNhs13358

Novel motifP-value
10.121
100.277
1000.618
1010.993
1020.958
1030.111
1040.691
1050.384
1060.0213
1070.124
1080.324
1090.285
110.0515
1100.0956
1110.0905
1120.116
1130.125
1140.032
1150.174
1160.125
1170.206
1180.475
1190.309
120.909
1200.0229
1210.631
1220.0764
1230.154
1240.787
1250.328
1260.308
1270.903
1280.0701
1290.366
130.486
1300.643
1310.751
1320.729
1330.987
1340.773
1350.312
1360.842
1370.402
1380.766
1390.402
140.866
1400.00286
1410.831
1420.578
1430.0169
1440.176
1450.148
1460.97
1470.263
1480.017
1490.0506
150.221
1500.135
1510.682
1520.0792
1530.838
1540.951
1550.187
1560.986
1570.383
1580.0408
1590.142
160.0451
1600.168
1610.808
1620.371
1630.803
1640.0713
1650.845
1660.407
1670.586
1680.366
1690.0348
170.134
180.108
190.0754
20.479
200.908
210.28
220.461
230.197
240.964
250.448
260.0823
270.313
280.547
290.0596
30.145
300.788
310.31
322.29153e-4
330.482
340.881
350.115
360.731
370.0194
380.697
390.325
40.976
400.704
410.699
420.778
430.179
440.0317
450.698
460.0348
470.23
480.272
490.483
50.42
500.63
510.752
520.702
530.37
540.595
550.338
560.679
570.13
580.914
590.0333
60.615
600.316
610.7
620.375
630.126
640.564
650.268
660.443
670.352
680.541
690.65
70.929
700.0812
710.145
720.725
730.0381
740.00617
750.43
760.581
770.0202
780.369
790.00312
80.0126
800.572
810.214
820.0752
830.976
840.552
850.0495
860.47
870.184
880.168
890.0982
90.499
900.0947
910.54
920.235
930.491
940.236
950.306
960.385
970.803
980.723
990.136



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: CNhs13358


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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