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FF:10042-101F6: 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 16:29, 29 March 2012


Name:corpus callosum, 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
tissuecorpus callosum
dev stage24-68 years old adult
sexmixed
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 number6080307
catalog numberCat:636567
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-Neural0.104
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-penis0.0801
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-0.364
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
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: CNhs10649

Jaspar motifP-value
MA0002.20.0413
MA0003.10.413
MA0004.10.316
MA0006.10.682
MA0007.10.4
MA0009.10.172
MA0014.10.722
MA0017.10.0185
MA0018.20.0439
MA0019.10.481
MA0024.10.705
MA0025.10.748
MA0027.10.378
MA0028.10.107
MA0029.10.25
MA0030.10.00107
MA0031.10.122
MA0035.20.24
MA0038.10.0201
MA0039.20.526
MA0040.10.18
MA0041.10.368
MA0042.10.595
MA0043.10.459
MA0046.10.367
MA0047.20.825
MA0048.10.0925
MA0050.10.166
MA0051.10.429
MA0052.10.0727
MA0055.10.00248
MA0057.10.864
MA0058.10.467
MA0059.10.05
MA0060.10.0209
MA0061.10.00268
MA0062.20.0361
MA0065.20.00307
MA0066.10.0122
MA0067.10.689
MA0068.10.997
MA0069.10.729
MA0070.10.148
MA0071.10.0323
MA0072.10.934
MA0073.10.63
MA0074.10.22
MA0076.10.284
MA0077.10.00129
MA0078.10.556
MA0079.20.363
MA0080.21.07771e-4
MA0081.10.0819
MA0083.10.379
MA0084.10.103
MA0087.10.026
MA0088.10.196
MA0090.10.303
MA0091.10.71
MA0092.10.334
MA0093.10.424
MA0099.23.97869e-13
MA0100.10.755
MA0101.10.00407
MA0102.20.245
MA0103.10.0393
MA0104.20.283
MA0105.12.70749e-6
MA0106.10.0146
MA0107.10.00298
MA0108.20.0188
MA0111.10.521
MA0112.20.00139
MA0113.10.439
MA0114.10.0201
MA0115.10.775
MA0116.16.48363e-4
MA0117.10.755
MA0119.10.0852
MA0122.10.369
MA0124.10.736
MA0125.10.152
MA0131.10.822
MA0135.10.00437
MA0136.11.48964e-6
MA0137.20.474
MA0138.20.248
MA0139.10.628
MA0140.10.197
MA0141.10.0152
MA0142.10.218
MA0143.10.0213
MA0144.10.592
MA0145.10.667
MA0146.10.0554
MA0147.10.116
MA0148.10.985
MA0149.10.00501
MA0150.13.3094e-4
MA0152.10.948
MA0153.10.875
MA0154.10.0346
MA0155.10.983
MA0156.16.06561e-4
MA0157.10.545
MA0159.10.0143
MA0160.10.0862
MA0162.10.16
MA0163.11.78658e-10
MA0164.10.612
MA0258.10.0243
MA0259.10.406



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: CNhs10649

Novel motifP-value
10.0322
100.0224
1000.265
1010.792
1020.857
1030.0721
1040.179
1050.535
1060.0349
1070.226
1080.757
1090.00708
110.00855
1100.0381
1110.0325
1120.245
1130.465
1140.0502
1150.563
1160.193
1170.0145
1180.129
1190.12
120.769
1200.083
1210.956
1220.596
1230.549
1240.349
1250.388
1260.181
1270.448
1280.191
1290.533
130.00857
1300.803
1310.017
1320.443
1330.00732
1340.147
1350.128
1360.0135
1370.769
1380.764
1390.127
140.868
1400.163
1410.105
1420.656
1430.00891
1440.824
1450.286
1460.939
1470.684
1480.339
1490.441
150.0478
1500.126
1510.878
1520.154
1530.692
1540.521
1550.421
1560.482
1570.419
1580.239
1590.00492
160.0498
1600.183
1610.285
1620.962
1630.759
1640.00332
1650.152
1660.93
1670.442
1680.819
1690.0272
170.115
180.0411
190.441
20.786
200.105
210.0432
220.494
230.443
240.183
250.495
260.00449
270.726
280.85
290.00364
30.0271
300.436
310.993
320.00929
330.0778
340.889
350.355
360.117
370.036
380.415
390.443
41
400.155
410.482
420.182
430.117
440.0203
450.975
460.0251
470.0731
480.0644
490.225
50.925
500.62
510.438
520.918
530.574
540.661
550.698
560.608
570.201
580.35
590.169
60.69
600.131
610.157
620.15
630.347
640.121
650.305
660.283
670.297
680.735
690.42
70.164
700.0103
710.00669
720.445
730.0599
740.411
750.0121
760.128
770.302
787.15873e-4
790.146
80.0624
800.569
810.334
820.519
830.205
840.381
850.363
860.184
870.0076
880.687
890.281
90.776
900.0184
910.425
920.335
930.998
940.0288
950.0273
960.82
970.853
980.126
990.967



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: CNhs10649


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)
0000073 (regional part of nervous system)
0000122 (neuron projection bundle)
0000153 (anterior region 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)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001018 (axon tract)
0001020 (nervous system commissure)
0001049 (neural tube)
0001062 (anatomical entity)
0001890 (forebrain)
0001893 (telencephalon)
0002050 (embryonic structure)
0002316 (white matter)
0002336 (corpus callosum)
0002346 (neurectoderm)
0002437 (cerebral hemisphere white matter)
0002473 (intercerebral commissure)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003544 (brain white matter)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005162 (multi cell component structure)
0005291 (embryonic tissue)
0005340 (dorsal telencephalic commissure)
0005423 (developing anatomical structure)
0005970 (brain commissure)
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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