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FF:10157-103A4: 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 17:15, 29 March 2012


Name:parietal lobe, adult, donor10252
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueparietal lobe
dev stageNA
sexfemale
age76
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
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-Neural0.389
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-penis1.061
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-0.284
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
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: CNhs12317

Jaspar motifP-value
MA0002.20.0356
MA0003.10.251
MA0004.10.342
MA0006.10.227
MA0007.10.298
MA0009.10.2
MA0014.10.651
MA0017.16.08332e-4
MA0018.20.441
MA0019.10.693
MA0024.10.89
MA0025.10.407
MA0027.10.567
MA0028.10.0452
MA0029.10.0325
MA0030.10.605
MA0031.10.972
MA0035.20.00473
MA0038.10.47
MA0039.20.105
MA0040.10.834
MA0041.10.437
MA0042.10.973
MA0043.10.981
MA0046.10.00124
MA0047.20.0757
MA0048.10.12
MA0050.10.0219
MA0051.10.0593
MA0052.10.838
MA0055.17.61174e-4
MA0057.10.825
MA0058.10.257
MA0059.10.0752
MA0060.10.99
MA0061.10.00848
MA0062.20.00139
MA0065.21.67388e-4
MA0066.10.0104
MA0067.10.926
MA0068.10.752
MA0069.10.578
MA0070.10.522
MA0071.10.0178
MA0072.10.272
MA0073.10.443
MA0074.10.215
MA0076.10.0769
MA0077.10.288
MA0078.10.723
MA0079.20.755
MA0080.25.66509e-8
MA0081.10.028
MA0083.10.00846
MA0084.10.845
MA0087.10.95
MA0088.10.181
MA0090.10.384
MA0091.10.47
MA0092.10.292
MA0093.10.344
MA0099.27.7007e-20
MA0100.10.55
MA0101.10.00256
MA0102.20.169
MA0103.10.194
MA0104.20.453
MA0105.10.00288
MA0106.10.0406
MA0107.10.00397
MA0108.20.156
MA0111.10.574
MA0112.20.0012
MA0113.10.52
MA0114.18.81304e-4
MA0115.10.296
MA0116.10.00943
MA0117.10.972
MA0119.10.119
MA0122.10.625
MA0124.10.539
MA0125.10.454
MA0131.10.978
MA0135.10.132
MA0136.11.29401e-12
MA0137.20.669
MA0138.20.361
MA0139.10.388
MA0140.16.72451e-4
MA0141.10.00302
MA0142.10.972
MA0143.10.968
MA0144.10.545
MA0145.10.161
MA0146.10.00956
MA0147.10.335
MA0148.10.0892
MA0149.10.0271
MA0150.13.9443e-4
MA0152.10.633
MA0153.10.0592
MA0154.10.0548
MA0155.10.515
MA0156.11.60029e-8
MA0157.10.703
MA0159.10.00524
MA0160.10.00734
MA0162.10.108
MA0163.15.26442e-5
MA0164.10.869
MA0258.10.0106
MA0259.10.91



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: CNhs12317

Novel motifP-value
10.0594
100.0553
1000.308
1010.573
1020.866
1030.13
1040.125
1050.127
1060.0433
1070.0941
1080.965
1090.00245
110.0124
1100.0458
1110.202
1120.49
1130.577
1140.204
1150.942
1160.138
1170.0103
1180.13
1190.225
120.46
1200.252
1210.276
1220.859
1230.62
1240.0833
1250.213
1260.0281
1270.452
1280.157
1290.599
135.95659e-4
1300.123
1310.0591
1320.666
1330.0812
1340.675
1350.157
1360.00129
1370.904
1380.968
1390.122
140.795
1400.57
1410.7
1420.773
1430.0874
1440.939
1450.102
1460.471
1470.728
1480.205
1490.228
150.112
1500.154
1510.624
1520.0768
1530.814
1540.457
1550.75
1560.452
1570.44
1580.227
1590.0244
160.0434
1600.236
1610.23
1620.732
1630.685
1640.0479
1650.0452
1660.894
1670.889
1680.426
1690.0104
170.133
180.143
190.186
20.851
200.125
210.0627
220.177
230.499
240.0293
250.514
261.51688e-4
270.812
280.608
290.0107
30.0531
300.974
310.856
320.0266
330.0477
340.606
350.679
360.168
370.0391
380.363
390.232
40.783
400.0239
410.289
420.247
430.12
440.203
450.658
460.0832
470.0594
480.049
490.21
50.689
500.333
510.388
520.474
530.911
540.332
550.672
560.436
570.377
580.377
590.0773
60.933
600.0749
610.0523
620.23
630.187
640.22
650.28
660.13
670.442
680.0948
690.323
70.0522
700.0494
710.0122
720.4
730.0268
740.781
750.0421
760.472
770.148
780.00284
790.402
80.0551
800.418
810.709
820.634
830.0323
840.666
850.274
860.235
877.28769e-5
880.82
890.408
90.329
900.135
910.921
920.613
930.93
940.206
950.0125
960.838
970.718
980.299
990.51



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: CNhs12317


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
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000153 (anterior region 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)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001872 (parietal lobe)
0001890 (forebrain)
0001893 (telencephalon)
0001950 (neocortex)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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