Personal tools

FF:11729-123E1: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 48: Line 48:
|profile_rnaseq=,,,
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|repeat_enrich_byfamily=-0.0630850568417265,0,0,0,0,0,0.109018938166599,0,0,0,0,0.50284783134463,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0.196747187304978,0,0,0,0,0,0,0.494089399417784,-0.449001713326725,0,0,0,0,0,0.0384291637369302,0,0.0191592509279852,0.520199839477486,0.794654388599397,0.269419612201536,0,0,0,0,0,0,0,0,0,0.109421078997306,0,0.043415531433866,0.269419612201536,0,0,0,0,0,0.269419612201536,0.269419612201536,0.331656786275404,0,-0.117389802908326,-0.310650657339386,0.0386561445338959,-0.104012827772446,0,-0.0682667324946745,-0.0286602088560886,-0.0617333749910964,0,0,-0.0152567643183588,0,0.128197204302579,-0.0788315948399074,0,0,0,0,0.054710539498653,0,0.0481760989644019,0.0517663399847592,0.021611941155193,0,0,0.109421078997306,0.331656786275404,0
|rna_box=123
|rna_box=123
|rna_catalog_number=custom
|rna_catalog_number=custom

Revision as of 10:22, 24 September 2012


Name:Mouse Cardiac Myocytes, donor2
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-ethanol-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} 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

CNhs12356

00
10
100
1000
10000.109
1001-0.0275
10020.24
1003-0.0137
10040
10050.00899
1006-0.00124
1007-0.0704
10080
10090.44
101-0.105
10100
1011-0.19
10120
10130.0706
10140.109
1015-0.116
10160.102
10170
10180
10190
1020
10200.478
10210
10220
10230
1024-0.14
10250
10260
10270
10280.109
1029-0.176
1030.634
10300
10310.666
10320.0691
10330
10340
10350
10360.026
10370
10380.255
1039-0.119
1040
10400.594
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



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: CNhs12356

Jaspar motifP-value
MA0002.20.307
MA0003.10.143
MA0004.10.5
MA0006.10.262
MA0007.10.0453
MA0009.10.977
MA0014.10.394
MA0017.10.01
MA0018.20.0134
MA0019.10.494
MA0024.11.75864e-4
MA0025.10.439
MA0027.10.363
MA0028.10.831
MA0029.10.897
MA0030.10.466
MA0031.10.881
MA0035.20.082
MA0038.10.467
MA0039.20.0325
MA0040.10.11
MA0041.10.779
MA0042.10.349
MA0043.10.207
MA0046.15.09613e-9
MA0047.20.112
MA0048.10.38
MA0050.10.065
MA0051.10.253
MA0052.10.748
MA0055.10.107
MA0057.10.0866
MA0058.10.177
MA0059.10.411
MA0060.13.20421e-13
MA0061.10.102
MA0062.20.282
MA0065.20.77
MA0066.10.943
MA0067.10.809
MA0068.10.0347
MA0069.10.683
MA0070.10.932
MA0071.10.213
MA0072.10.481
MA0073.10.557
MA0074.10.37
MA0076.10.228
MA0077.10.181
MA0078.10.778
MA0079.20.00109
MA0080.20.707
MA0081.10.624
MA0083.11.75853e-5
MA0084.10.642
MA0087.10.846
MA0088.10.482
MA0090.13.70177e-5
MA0091.10.113
MA0092.10.133
MA0093.10.513
MA0099.27.41901e-4
MA0100.10.368
MA0101.10.0168
MA0102.20.748
MA0103.16.68462e-7
MA0104.20.102
MA0105.10.415
MA0106.10.01
MA0107.10.0198
MA0108.20.501
MA0111.10.816
MA0112.20.0184
MA0113.10.111
MA0114.10.0207
MA0115.10.0484
MA0116.10.745
MA0117.10.33
MA0119.10.409
MA0122.10.885
MA0124.10.502
MA0125.10.0165
MA0131.10.333
MA0135.10.394
MA0136.10.664
MA0137.20.073
MA0138.20.0293
MA0139.10.451
MA0140.10.235
MA0141.10.224
MA0142.10.0247
MA0143.10.581
MA0144.10.00969
MA0145.10.0343
MA0146.10.0295
MA0147.10.0887
MA0148.10.202
MA0149.10.806
MA0150.10.0936
MA0152.10.0105
MA0153.11.59794e-8
MA0154.10.0119
MA0155.10.402
MA0156.10.543
MA0157.10.347
MA0159.10.818
MA0160.10.172
MA0162.10.162
MA0163.10.156
MA0164.10.976
MA0258.10.866
MA0259.10.768



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: CNhs12356

Novel motifP-value
10.952
100.584
1000.911
1010.513
1020.602
1030.86
1040.735
1050.3
1060.0202
1070.152
1080.595
1090.00324
110.272
1100.115
1110.941
1120.358
1130.451
1140.293
1150.612
1160.167
1170.404
1180.934
1190.888
120.576
1200.469
1210.587
1220.463
1230.577
1240.142
1250.438
1260.567
1270.169
1280.111
1290.61
130.0924
1300.418
1310.138
1320.92
1330.911
1340.838
1350.716
1360.152
1370.482
1380.624
1390.631
140.704
1400.307
1410.0999
1420.977
1430.15
1440.119
1450.406
1460.864
1470.524
1480.683
1490.00115
150.247
1500.0416
1510.584
1520.0189
1530.674
1540.431
1550.9
1561.08024e-37
1570.602
1580.156
1590.0066
1600.407
1610.553
1620.59
1630.546
1640.184
1650.825
1660.49
1670.388
1680.933
1690.0148
170.254
180.483
190.0134
20.173
200.649
210.311
220.054
230.697
240.235
250.229
260.0452
270.503
280.586
290.171
30.455
300.845
310.79
320.126
330.491
340.747
350.0634
360.283
370.0556
380.934
390.276
40.836
400.675
410.761
420.599
430.052
440.7
450.573
460.908
470.44
480.612
490.813
50.3
500.0787
510.821
520.318
530.829
540.549
550.861
560.633
570.884
580.362
590.00715
60.335
600.349
610.544
620.494
630.234
640.696
650.647
660.698
670.409
680.228
690.777
70.667
700.0733
710.595
720.639
730.00961
740.617
750.286
760.988
770.0232
780.0667
790.656
80.467
800.0803
810.905
820.381
830.34
840.86
850.103
860.724
870.0114
880.796
890.346
90.557
900.741
910.957
920.166
930.555
940.662
950.00825
960.0271
970.215
980.437
990.914



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: CNhs12356


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)
0000548 (animal cell)
0002371 (somatic cell)
0000393 (electrically responsive cell)
0000183 (contractile cell)
0000187 (muscle cell)
0000211 (electrically active cell)
0000255 (eukaryotic cell)
0002494 (cardiocyte)
0000737 (striated muscle cell)
0000746 (cardiac muscle cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0007100 (primary circulatory organ)
0000948 (heart)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0010317 (germ layer / neural crest derived structure)
0004535 (cardiovascular system)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000106 (mouse cardiac myocyte sample)

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
CL:0000355 (multi-potent skeletal muscle stem cell)
CL:0000222 (mesodermal cell)
CL:0000513 (cardiac muscle myoblast)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11729-123E1&oldid=2141394"