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FF:11335-117F3: 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 17:04, 29 March 2012


Name:Smooth Muscle Cells - Prostate, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueprostate
dev stage34 years old adult
sexmale
age34
cell typesmooth muscle cell
cell lineNA
companyLonza
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-penis0.162
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-0.137
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: CNhs11976

Jaspar motifP-value
MA0002.20.0442
MA0003.10.583
MA0004.10.0655
MA0006.10.129
MA0007.10.948
MA0009.10.449
MA0014.10.103
MA0017.10.423
MA0018.24.17417e-5
MA0019.10.163
MA0024.10.00865
MA0025.19.43535e-4
MA0027.10.802
MA0028.10.719
MA0029.10.515
MA0030.10.0748
MA0031.10.0626
MA0035.20.26
MA0038.10.0371
MA0039.20.00311
MA0040.10.528
MA0041.10.517
MA0042.10.602
MA0043.10.00817
MA0046.10.0641
MA0047.20.136
MA0048.10.164
MA0050.10.0936
MA0051.10.0534
MA0052.14.03618e-5
MA0055.10.673
MA0057.10.439
MA0058.10.0161
MA0059.10.78
MA0060.16.00621e-7
MA0061.10.109
MA0062.20.00155
MA0065.20.541
MA0066.10.614
MA0067.10.00641
MA0068.10.55
MA0069.10.119
MA0070.10.98
MA0071.10.568
MA0072.10.203
MA0073.10.973
MA0074.10.0368
MA0076.10.272
MA0077.10.673
MA0078.10.679
MA0079.20.64
MA0080.26.94865e-9
MA0081.10.00799
MA0083.10.686
MA0084.10.239
MA0087.10.923
MA0088.10.266
MA0090.10.0796
MA0091.13.43923e-4
MA0092.10.722
MA0093.10.0588
MA0099.21.93996e-8
MA0100.10.0712
MA0101.10.00232
MA0102.20.468
MA0103.10.0177
MA0104.20.0426
MA0105.10.747
MA0106.10.117
MA0107.10.00249
MA0108.20.355
MA0111.10.702
MA0112.20.0201
MA0113.10.941
MA0114.10.827
MA0115.10.212
MA0116.10.094
MA0117.10.549
MA0119.10.25
MA0122.10.158
MA0124.10.0737
MA0125.10.293
MA0131.10.717
MA0135.10.0303
MA0136.12.57107e-12
MA0137.20.766
MA0138.20.88
MA0139.10.606
MA0140.10.255
MA0141.10.646
MA0142.10.0301
MA0143.10.762
MA0144.10.646
MA0145.10.522
MA0146.10.0875
MA0147.10.144
MA0148.10.274
MA0149.10.617
MA0150.10.0309
MA0152.10.434
MA0153.10.797
MA0154.10.65
MA0155.10.165
MA0156.12.46623e-9
MA0157.10.0813
MA0159.10.966
MA0160.10.243
MA0162.10.217
MA0163.15.47243e-4
MA0164.10.434
MA0258.10.224
MA0259.10.298



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: CNhs11976

Novel motifP-value
10.654
100.52
1000.0671
1010.482
1020.287
1030.696
1040.876
1050.0187
1060.698
1070.39
1080.4
1090.556
110.431
1100.384
1110.712
1120.402
1130.0293
1140.483
1150.00116
1160.0214
1170.517
1180.837
1190.393
120.187
1200.206
1210.0666
1220.00341
1230.319
1240.271
1250.247
1260.738
1270.177
1280.185
1290.112
130.965
1300.917
1310.322
1320.378
1330.809
1340.891
1350.943
1360.0925
1370.0638
1380.939
1390.0881
140.171
1400.998
1410.598
1420.957
1430.884
1440.182
1450.31
1460.482
1470.583
1480.672
1490.0116
150.239
1500.287
1510.558
1520.0185
1530.382
1540.985
1550.0836
1560.319
1570.184
1580.0125
1590.577
160.0376
1600.929
1610.671
1620.47
1630.729
1640.00584
1650.729
1660.112
1670.744
1680.544
1690.0257
170.942
180.318
190.00648
20.328
200.635
210.134
220.278
230.919
240.346
250.0561
260.296
270.887
280.0914
290.306
30.516
300.939
310.738
324.51469e-18
330.657
340.881
350.402
360.0506
370.0385
380.193
390.519
40.118
400.235
410.0901
420.57
430.936
440.109
450.384
460.509
470.606
480.89
490.359
50.588
500.794
510.666
520.94
530.312
540.701
550.624
560.94
570.932
580.228
590.169
60.594
600.657
610.664
620.617
630.522
640.68
650.998
660.2
670.757
680.818
690.997
70.0755
700.942
710.173
720.517
730.00413
740.0785
750.373
760.823
770.244
780.208
790.00235
80.123
800.0131
810.879
820.383
830.255
840.75
850.416
860.215
870.0821
880.608
890.2
90.956
900.597
910.634
920.392
930.314
940.732
950.1
960.37
970.84
980.381
990.00175



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: CNhs11976


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)
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)
1000487 (smooth muscle cell of prostate)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000079 (male reproductive system)
0000119 (cell layer)
0000161 (orifice)
0000162 (cloaca)
0000163 (embryonic cloaca)
0000164 (primitive urogenital sinus)
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)
0000925 (endoderm)
0000926 (mesoderm)
0000990 (reproductive system)
0001007 (digestive system)
0001015 (musculature)
0001046 (hindgut)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001353 (anal region)
0001555 (digestive tract)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002367 (prostate gland)
0002385 (muscle tissue)
0002530 (gland)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003064 (intermediate mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003101 (male organism)
0003104 (mesenchyme)
0003353 (epithelium of hindgut)
0003820 (prostate bud)
0003929 (gut epithelium)
0003937 (sex gland)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004122 (genitourinary system)
0004185 (endodermal part of digestive tract)
0004290 (dermomyotome)
0004902 (urogenital sinus epithelium)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005156 (reproductive structure)
0005291 (embryonic tissue)
0005399 (male reproductive gland)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006866 (terminal part of digestive tract)
0007026 (primitive gut)
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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