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|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=10.00000
|rna_weight_ug=10
|rna_concentration=1ug/ul
|rna_concentration=1ug/ul
|sample_note=
|sample_note=
|profile_hcage=CNhs12355,LSID913,release011,MAPPING
|profile_hcage=CNhs12355,LSID913,release011,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:48, 27 February 2012


Name:Mouse Cardiac Myocytes, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueheart
dev stageNA
sexNA
ageNA
cell typecardiac muscle cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs12355

00
10
100
1000
10000.0639
1001-0.00986
10020.425
10030.14
10040
10050
1006-0.302
1007-0.201
10080
10090.56
101-0.0743
10100
1011-0.198
10120
10130.0555
10140.00488
1015-0.0304
10160.106
10170
10180
10190
1020
10200.18
10210.0994
1022-0.0704
10230
1024-0.14
10250
10260
10270
10280.0994
1029-0.12
1030.549
10300
10310.732
10320.0785
1033-0.0752
10340
10350
1036-0.0803
10370
1038-5.64625e-4
1039-0.154
1040
10400.526
10410



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: CNhs12355

Jaspar motifP-value
MA0002.20.314
MA0003.10.305
MA0004.10.863
MA0006.10.203
MA0007.10.00826
MA0009.10.735
MA0014.10.392
MA0017.10.00911
MA0018.20.0607
MA0019.10.458
MA0024.10.00165
MA0025.10.727
MA0027.10.187
MA0028.10.11
MA0029.10.806
MA0030.10.209
MA0031.10.43
MA0035.20.0121
MA0038.10.1
MA0039.20.115
MA0040.10.0315
MA0041.10.473
MA0042.10.686
MA0043.10.54
MA0046.13.88064e-9
MA0047.20.0084
MA0048.10.0733
MA0050.10.0038
MA0051.10.125
MA0052.10.27
MA0055.10.0107
MA0057.10.0583
MA0058.10.648
MA0059.10.64
MA0060.11.52606e-10
MA0061.10.131
MA0062.20.0877
MA0065.20.807
MA0066.10.492
MA0067.10.841
MA0068.10.0423
MA0069.10.238
MA0070.10.626
MA0071.10.569
MA0072.10.923
MA0073.10.332
MA0074.10.503
MA0076.10.571
MA0077.10.846
MA0078.10.496
MA0079.20.00735
MA0080.20.289
MA0081.10.708
MA0083.11.65715e-4
MA0084.10.545
MA0087.10.712
MA0088.10.516
MA0090.12.72667e-4
MA0091.10.0523
MA0092.10.164
MA0093.10.812
MA0099.25.91583e-9
MA0100.10.985
MA0101.10.0114
MA0102.20.646
MA0103.16.49974e-7
MA0104.20.239
MA0105.10.405
MA0106.14.17265e-4
MA0107.10.0249
MA0108.20.0793
MA0111.10.927
MA0112.20.0181
MA0113.10.0218
MA0114.10.02
MA0115.10.0909
MA0116.10.776
MA0117.10.238
MA0119.10.171
MA0122.10.745
MA0124.10.253
MA0125.10.0292
MA0131.10.559
MA0135.10.343
MA0136.10.35
MA0137.20.299
MA0138.20.00114
MA0139.10.432
MA0140.10.0253
MA0141.10.287
MA0142.10.012
MA0143.10.709
MA0144.10.0091
MA0145.10.0534
MA0146.10.0195
MA0147.10.263
MA0148.10.0864
MA0149.10.966
MA0150.10.00453
MA0152.10.827
MA0153.13.88925e-8
MA0154.10.0423
MA0155.10.915
MA0156.10.0268
MA0157.10.386
MA0159.10.171
MA0160.10.269
MA0162.10.195
MA0163.10.174
MA0164.10.706
MA0258.10.565
MA0259.10.983



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: CNhs12355

Novel motifP-value
10.879
100.222
1000.478
1010.395
1020.128
1030.817
1040.233
1050.402
1060.0116
1070.369
1080.564
1090.0228
110.474
1100.199
1110.856
1120.94
1130.471
1140.282
1150.957
1160.0829
1170.0643
1180.886
1190.679
120.912
1200.402
1210.353
1220.0654
1230.795
1240.494
1250.118
1260.119
1270.0399
1280.0261
1290.241
130.0737
1300.991
1310.0884
1320.188
1330.201
1340.82
1350.756
1360.033
1370.718
1380.904
1390.817
140.334
1400.507
1410.318
1420.826
1430.0755
1440.217
1450.237
1460.717
1470.315
1480.983
1490.00557
150.128
1500.041
1510.612
1520.00866
1530.744
1540.768
1550.186
1560.997
1570.451
1580.698
1590.0776
1600.924
1610.471
1620.392
1630.436
1640.296
1650.37
1660.761
1670.539
1680.709
1690.0198
170.32
180.36
190.0392
20.383
200.221
210.14
220.139
230.324
240.0677
250.154
260.0479
270.287
280.61
290.0278
30.377
300.36
310.807
320.154
330.95
340.957
350.255
360.556
370.0312
380.423
390.164
40.323
400.684
410.992
420.543
430.0674
440.337
450.931
460.657
470.722
480.942
490.92
50.933
500.11
510.696
520.528
530.735
540.546
550.987
560.819
570.796
580.534
590.0171
60.429
600.465
610.362
620.954
630.352
640.37
650.224
660.796
670.81
680.145
690.984
70.957
700.0158
710.2
720.771
730.0016
740.464
750.161
760.667
770.0415
780.023
790.223
80.623
800.0224
810.819
820.987
830.629
840.854
850.145
860.572
870.00877
880.297
890.78
90.774
900.881
910.523
920.0978
930.575
940.796
950.00142
960.203
970.264
980.406
990.898



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: CNhs12355


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000393 (electrically responsive cell)
0000513 (cardiac muscle myoblast)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0000737 (striated muscle cell)
0000746 (cardiac muscle cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002494 (cardiocyte)

UBERON: Anatomy
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001015 (musculature)
0001048 (primordium)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003081 (lateral plate mesoderm)
0003082 (myotome)
0003084 (heart primordium)
0003104 (mesenchyme)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004290 (dermomyotome)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0007005 (cardiac mesoderm)
0007100 (primary circulatory organ)
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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