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FF:10035-101E8: 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 16:28, 29 March 2012


Name:paracentral gyrus, 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
tissueparacentral gyrus
dev stage22-69 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 number3040378
catalog numberCat:636574
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-Neural0.346
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-penis0.13
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-0.342
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.055
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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: CNhs10642

Jaspar motifP-value
MA0002.20.00816
MA0003.10.376
MA0004.10.457
MA0006.10.392
MA0007.10.194
MA0009.10.18
MA0014.10.681
MA0017.10.0047
MA0018.20.0535
MA0019.10.811
MA0024.10.99
MA0025.10.217
MA0027.10.489
MA0028.10.12
MA0029.10.138
MA0030.10.179
MA0031.10.962
MA0035.20.135
MA0038.10.0511
MA0039.20.242
MA0040.10.435
MA0041.10.278
MA0042.10.657
MA0043.10.379
MA0046.10.124
MA0047.20.0881
MA0048.10.103
MA0050.10.00631
MA0051.10.117
MA0052.10.108
MA0055.10.00281
MA0057.10.948
MA0058.10.422
MA0059.10.0842
MA0060.10.227
MA0061.10.00938
MA0062.20.0293
MA0065.24.35621e-4
MA0066.10.0328
MA0067.10.676
MA0068.10.4
MA0069.10.455
MA0070.10.0808
MA0071.10.0374
MA0072.10.447
MA0073.10.354
MA0074.10.194
MA0076.10.292
MA0077.10.191
MA0078.10.873
MA0079.20.4
MA0080.22.79766e-8
MA0081.10.0572
MA0083.10.102
MA0084.10.646
MA0087.10.378
MA0088.10.138
MA0090.10.251
MA0091.10.434
MA0092.10.367
MA0093.10.496
MA0099.21.0312e-10
MA0100.10.7
MA0101.10.00515
MA0102.20.162
MA0103.10.232
MA0104.20.437
MA0105.15.29358e-4
MA0106.10.0343
MA0107.10.00853
MA0108.20.311
MA0111.10.453
MA0112.29.93903e-4
MA0113.10.278
MA0114.10.00388
MA0115.10.404
MA0116.10.0035
MA0117.10.957
MA0119.10.0412
MA0122.10.798
MA0124.10.711
MA0125.10.241
MA0131.10.893
MA0135.10.0222
MA0136.14.27816e-10
MA0137.20.561
MA0138.20.181
MA0139.10.398
MA0140.10.0159
MA0141.10.0158
MA0142.10.969
MA0143.10.939
MA0144.10.304
MA0145.10.23
MA0146.10.0101
MA0147.10.31
MA0148.10.0887
MA0149.10.0168
MA0150.10.00276
MA0152.10.919
MA0153.10.452
MA0154.10.0412
MA0155.10.666
MA0156.12.09071e-5
MA0157.10.6
MA0159.10.00594
MA0160.10.0478
MA0162.10.119
MA0163.13.28329e-6
MA0164.10.731
MA0258.10.0102
MA0259.10.756



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: CNhs10642

Novel motifP-value
10.033
100.0256
1000.261
1010.896
1020.792
1030.23
1040.147
1050.299
1060.058
1070.129
1080.829
1090.01
110.0149
1100.0367
1110.0667
1120.335
1130.662
1140.0895
1150.951
1160.165
1170.00907
1180.0982
1190.108
120.753
1200.136
1210.674
1220.537
1230.57
1240.0275
1250.164
1260.029
1270.493
1280.171
1290.538
130.00119
1300.519
1310.0669
1320.775
1330.0015
1340.262
1350.162
1360.0145
1370.763
1380.833
1390.0991
140.884
1400.114
1410.26
1420.854
1430.0142
1440.88
1450.0782
1460.624
1470.973
1480.127
1490.279
150.0707
1500.181
1510.649
1520.149
1530.737
1540.616
1550.379
1560.389
1570.401
1580.719
1590.0483
160.0707
1600.184
1610.169
1620.976
1630.83
1640.0168
1650.0443
1660.863
1670.335
1680.72
1690.00757
170.154
180.192
190.204
20.997
200.0904
210.077
220.25
230.452
240.108
250.486
266.70521e-5
270.976
280.703
290.0113
30.0263
300.591
310.89
320.0271
330.0685
340.774
350.476
360.086
370.0451
380.309
390.241
40.922
400.0511
410.425
420.176
430.106
440.0892
450.812
460.0497
470.0621
480.0526
490.131
50.486
500.356
510.526
520.64
530.967
540.484
550.359
560.484
570.243
580.309
590.137
60.561
600.0805
610.0729
620.17
630.158
640.213
650.278
660.303
670.355
680.335
690.404
70.0568
700.0186
710.0086
720.507
730.0486
740.638
750.0292
760.383
770.215
780.00308
790.168
80.0509
800.993
810.544
820.453
830.173
840.661
850.259
860.213
870.00841
880.868
890.535
90.521
900.0355
910.429
920.487
930.601
940.0513
950.0333
960.844
970.759
980.206
990.812



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: CNhs10642


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)
0000200 (gyrus)
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)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001890 (forebrain)
0001893 (telencephalon)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
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)
0007190 (paracentral gyrus)
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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