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FF:10034-101E7: 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:parietal lobe, 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
tissueparietal lobe
dev stage35-89 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 number636571
catalog numberCat:636571
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-Neural0.331
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-penis0.136
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-0.368
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0519
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs10641

Jaspar motifP-value
MA0002.20.00839
MA0003.10.383
MA0004.10.481
MA0006.10.393
MA0007.10.218
MA0009.10.247
MA0014.10.694
MA0017.10.00361
MA0018.20.0422
MA0019.10.705
MA0024.10.968
MA0025.10.171
MA0027.10.519
MA0028.10.108
MA0029.10.167
MA0030.10.0993
MA0031.10.812
MA0035.20.141
MA0038.10.0379
MA0039.20.277
MA0040.10.361
MA0041.10.161
MA0042.10.597
MA0043.10.314
MA0046.10.0925
MA0047.20.146
MA0048.10.105
MA0050.10.00307
MA0051.10.0724
MA0052.10.0587
MA0055.10.00375
MA0057.10.948
MA0058.10.449
MA0059.10.0794
MA0060.10.179
MA0061.10.00904
MA0062.20.0277
MA0065.25.6965e-4
MA0066.10.0291
MA0067.10.687
MA0068.10.37
MA0069.10.517
MA0070.10.0492
MA0071.10.0399
MA0072.10.52
MA0073.10.368
MA0074.10.18
MA0076.10.27
MA0077.10.177
MA0078.10.874
MA0079.20.375
MA0080.26.0115e-8
MA0081.10.0613
MA0083.10.163
MA0084.10.606
MA0087.10.327
MA0088.10.144
MA0090.10.264
MA0091.10.415
MA0092.10.386
MA0093.10.521
MA0099.22.45716e-10
MA0100.10.69
MA0101.10.00595
MA0102.20.172
MA0103.10.22
MA0104.20.428
MA0105.13.64246e-4
MA0106.10.0305
MA0107.10.00959
MA0108.20.318
MA0111.10.432
MA0112.20.00104
MA0113.10.297
MA0114.10.00409
MA0115.10.342
MA0116.10.00304
MA0117.10.946
MA0119.10.0489
MA0122.10.869
MA0124.10.704
MA0125.10.253
MA0131.10.927
MA0135.10.0158
MA0136.17.19597e-10
MA0137.20.504
MA0138.20.171
MA0139.10.394
MA0140.10.016
MA0141.10.0159
MA0142.10.82
MA0143.10.795
MA0144.10.278
MA0145.10.251
MA0146.10.0132
MA0147.10.295
MA0148.10.127
MA0149.10.0157
MA0150.10.00381
MA0152.10.981
MA0153.10.389
MA0154.10.0392
MA0155.10.696
MA0156.12.19848e-5
MA0157.10.724
MA0159.10.00566
MA0160.10.0509
MA0162.10.119
MA0163.11.42459e-6
MA0164.10.754
MA0258.10.0115
MA0259.10.724



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: CNhs10641

Novel motifP-value
10.0314
100.0228
1000.256
1010.914
1020.784
1030.182
1040.183
1050.348
1060.0595
1070.126
1080.829
1090.00959
110.0143
1100.0385
1110.063
1120.289
1130.666
1140.0835
1150.918
1160.18
1170.00892
1180.0963
1190.104
120.799
1200.13
1210.682
1220.549
1230.619
1240.0302
1250.153
1260.0324
1270.484
1280.154
1290.544
130.00135
1300.551
1310.0619
1320.716
1330.00304
1340.259
1350.15
1360.0103
1370.794
1380.822
1390.0699
140.898
1400.141
1410.221
1420.896
1430.0151
1440.805
1450.0786
1460.664
1470.976
1480.142
1490.293
150.0757
1500.184
1510.663
1520.155
1530.741
1540.602
1550.366
1560.484
1570.431
1580.788
1590.0722
160.067
1600.194
1610.189
1620.965
1630.929
1640.0161
1650.0265
1660.773
1670.304
1680.694
1690.00772
170.161
180.186
190.208
20.989
200.097
210.0816
220.271
230.463
240.109
250.482
267.12615e-5
270.969
280.7
290.00977
30.0247
300.592
310.907
320.0266
330.0718
340.836
350.473
360.0901
370.0396
380.324
390.264
40.977
400.0589
410.457
420.168
430.106
440.0782
450.828
460.0455
470.0608
480.0534
490.137
50.465
500.371
510.514
520.627
530.916
540.506
550.351
560.477
570.23
580.297
590.134
60.562
600.0792
610.0648
620.163
630.17
640.21
650.29
660.311
670.33
680.377
690.381
70.0611
700.0211
710.00733
720.468
730.0508
740.655
750.0293
760.363
770.231
780.00291
790.172
80.0463
800.989
810.532
820.446
830.163
840.63
850.232
860.211
870.00851
880.867
890.531
90.544
900.0326
910.435
920.464
930.701
940.0573
950.0291
960.965
970.774
980.196
990.784



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: CNhs10641


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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