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FF:10048-101G3: 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 16:51, 29 March 2012


Name:smooth muscle, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesmooth muscle
dev stage20-68 years old adult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number9052728A
catalog numberCat:636547
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-penis0.172
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-0.369
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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: CNhs11755

Jaspar motifP-value
MA0002.20.00203
MA0003.10.883
MA0004.10.00874
MA0006.10.955
MA0007.10.115
MA0009.10.478
MA0014.10.182
MA0017.10.103
MA0018.20.318
MA0019.10.805
MA0024.10.00942
MA0025.10.155
MA0027.10.355
MA0028.18.4276e-7
MA0029.10.145
MA0030.10.0686
MA0031.10.0278
MA0035.20.273
MA0038.10.159
MA0039.20.0196
MA0040.10.805
MA0041.10.772
MA0042.10.59
MA0043.10.0348
MA0046.10.313
MA0047.20.478
MA0048.10.476
MA0050.10.987
MA0051.10.191
MA0052.10.00401
MA0055.11.18465e-4
MA0057.10.947
MA0058.10.00191
MA0059.11.40039e-4
MA0060.15.62475e-7
MA0061.10.00133
MA0062.21.09545e-12
MA0065.20.0231
MA0066.10.00176
MA0067.10.326
MA0068.10.188
MA0069.10.766
MA0070.10.0993
MA0071.10.15
MA0072.10.124
MA0073.10.332
MA0074.10.909
MA0076.11.35825e-8
MA0077.10.197
MA0078.10.193
MA0079.20.679
MA0080.27.71595e-7
MA0081.10.0102
MA0083.11.88499e-14
MA0084.10.883
MA0087.10.926
MA0088.10.165
MA0090.10.0386
MA0091.10.164
MA0092.10.211
MA0093.10.00537
MA0099.22.2029e-21
MA0100.10.0358
MA0101.10.00235
MA0102.20.152
MA0103.10.0237
MA0104.23.867e-4
MA0105.11.39397e-6
MA0106.10.0709
MA0107.17.00303e-4
MA0108.26.88836e-6
MA0111.10.959
MA0112.20.0126
MA0113.10.715
MA0114.10.00606
MA0115.10.141
MA0116.14.328e-4
MA0117.10.471
MA0119.10.997
MA0122.10.914
MA0124.10.313
MA0125.10.575
MA0131.10.353
MA0135.10.436
MA0136.16.39458e-12
MA0137.20.924
MA0138.20.269
MA0139.10.17
MA0140.10.0653
MA0141.10.0282
MA0142.10.014
MA0143.10.726
MA0144.10.901
MA0145.10.416
MA0146.10.156
MA0147.11.17154e-4
MA0148.10.289
MA0149.10.105
MA0150.16.19699e-5
MA0152.10.526
MA0153.10.821
MA0154.10.00917
MA0155.10.823
MA0156.11.57829e-12
MA0157.10.283
MA0159.10.127
MA0160.10.0911
MA0162.10.311
MA0163.18.51351e-5
MA0164.10.467
MA0258.10.0141
MA0259.10.0348



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: CNhs11755

Novel motifP-value
10.0479
100.234
1000.115
1010.434
1020.221
1030.0556
1040.459
1050.586
1060.403
1070.334
1080.861
1090.00398
110.0572
1100.16
1110.0742
1120.67
1130.196
1140.0624
1150.322
1160.128
1170.0138
1180.0596
1190.714
120.227
1200.0666
1210.253
1220.0847
1230.923
1240.654
1250.528
1260.734
1270.528
1280.464
1290.499
130.059
1300.738
1310.322
1320.0355
1330.166
1340.253
1350.135
1360.263
1370.556
1380.986
1390.869
140.896
1400.913
1410.794
1420.965
1430.00356
1440.325
1450.783
1460.379
1470.491
1480.397
1490.21
150.0145
1500.394
1510.773
1520.218
1530.0824
1540.872
1550.486
1560.246
1570.676
1580.606
1590.625
160.16
1600.751
1610.508
1620.589
1630.39
1640.11
1650.46
1660.0817
1670.231
1680.948
1690.392
170.449
180.0691
190.265
20.0603
200.0808
210.538
220.881
230.734
240.117
250.16
260.0678
270.765
280.479
290.00156
30.321
300.148
310.996
320.489
330.117
340.533
350.375
360.00846
370.13
380.503
390.405
40.127
400.00904
410.0199
420.253
430.274
440.967
450.492
460.19
470.059
480.171
490.378
50.682
500.798
510.553
520.31
530.709
540.996
550.77
560.659
570.476
580.58
590.464
60.639
600.856
610.286
620.389
630.409
640.177
650.782
660.00135
670.838
680.121
690.743
70.123
700.572
710.0475
720.621
730.0389
740.447
750.0208
760.189
770.433
780.102
790.333
80.191
800.0495
810.369
820.886
830.896
840.874
850.534
860.831
871.03148e-4
880.91
890.628
90.805
900.202
910.0499
920.57
930.013
940.0594
955.65349e-5
960.491
970.86
980.492
990.307



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: CNhs11755


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

UBERON: Anatomy
0000061 (anatomical structure)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001015 (musculature)
0001062 (anatomical entity)
0001135 (smooth muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0005423 (developing anatomical structure)
0007023 (adult organism)

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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