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FF:11574-120E8: 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 17:24, 29 March 2012


Name:Neurons, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3153
catalog numberSC1525
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-Neural0.369
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-penis-0.106
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-lymphoma0.187
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12726

Jaspar motifP-value
MA0002.25.908e-5
MA0003.10.162
MA0004.10.522
MA0006.10.415
MA0007.10.164
MA0009.10.197
MA0014.10.717
MA0017.10.00251
MA0018.20.00423
MA0019.10.882
MA0024.10.00413
MA0025.10.509
MA0027.10.138
MA0028.10.945
MA0029.10.0619
MA0030.10.594
MA0031.10.0882
MA0035.20.0542
MA0038.11.68336e-5
MA0039.20.213
MA0040.10.716
MA0041.10.547
MA0042.10.712
MA0043.10.254
MA0046.10.524
MA0047.20.00491
MA0048.10.659
MA0050.13.71735e-7
MA0051.10.0074
MA0052.10.385
MA0055.10.247
MA0057.10.266
MA0058.10.432
MA0059.10.216
MA0060.15.67641e-7
MA0061.10.027
MA0062.20.574
MA0065.24.92644e-4
MA0066.10.0534
MA0067.10.664
MA0068.10.00178
MA0069.10.399
MA0070.10.0122
MA0071.10.07
MA0072.10.748
MA0073.10.453
MA0074.10.208
MA0076.10.361
MA0077.10.0281
MA0078.10.344
MA0079.20.618
MA0080.21.30342e-9
MA0081.10.0676
MA0083.10.994
MA0084.10.117
MA0087.10.677
MA0088.10.381
MA0090.10.105
MA0091.10.47
MA0092.10.873
MA0093.10.58
MA0099.21.23665e-9
MA0100.10.297
MA0101.10.0157
MA0102.20.0208
MA0103.10.096
MA0104.20.805
MA0105.10.0151
MA0106.10.0546
MA0107.10.0231
MA0108.20.023
MA0111.10.532
MA0112.21.28981e-4
MA0113.10.081
MA0114.10.0124
MA0115.10.16
MA0116.10.0242
MA0117.10.775
MA0119.10.103
MA0122.10.399
MA0124.10.542
MA0125.10.0201
MA0131.10.707
MA0135.10.00146
MA0136.19.67278e-7
MA0137.20.424
MA0138.20.252
MA0139.10.353
MA0140.10.00454
MA0141.10.00634
MA0142.10.0193
MA0143.10.0376
MA0144.10.209
MA0145.10.162
MA0146.10.00759
MA0147.10.631
MA0148.10.0167
MA0149.10.00384
MA0150.12.50571e-4
MA0152.10.336
MA0153.10.537
MA0154.10.045
MA0155.10.663
MA0156.14.10774e-4
MA0157.10.0277
MA0159.10.00206
MA0160.10.0212
MA0162.10.271
MA0163.14.3358e-5
MA0164.10.568
MA0258.10.00754
MA0259.10.987



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: CNhs12726

Novel motifP-value
10.0642
100.0722
1000.58
1010.638
1020.973
1030.249
1040.206
1050.297
1060.014
1070.0806
1080.784
1090.0033
110.0314
1100.214
1110.0859
1120.0938
1130.938
1140.00996
1150.814
1160.368
1170.0297
1180.191
1190.105
120.802
1200.816
1210.432
1220.947
1230.767
1240.195
1250.809
1260.00845
1270.267
1280.156
1290.434
130.00813
1300.831
1310.9
1320.956
1330.221
1340.493
1350.615
1360.0117
1370.557
1380.51
1390.0361
140.803
1400.257
1410.487
1420.978
1430.0155
1440.43
1450.512
1460.814
1470.732
1480.0221
1490.125
150.0914
1500.254
1510.363
1520.0288
1530.87
1540.837
1550.255
1560.649
1570.662
1580.566
1590.824
160.0589
1600.131
1610.0976
1620.749
1630.22
1640.0093
1650.813
1660.674
1670.258
1680.298
1690.00589
170.0616
180.344
190.131
20.558
200.5
210.11
220.123
230.0965
240.18
250.578
260.0144
270.576
280.782
290.0482
30.0378
300.967
310.884
320.0274
330.348
340.69
350.631
360.257
370.0236
380.225
390.203
40.606
400.112
410.566
420.207
430.127
440.0948
450.667
460.172
470.138
480.0937
490.14
50.233
500.325
510.423
520.371
530.614
540.273
550.187
560.321
570.255
580.164
590.0352
60.829
600.0522
610.0255
620.121
630.117
640.45
650.17
660.942
670.77
680.459
690.367
70.13
700.0535
710.015
720.396
730.0156
740.715
750.0346
760.367
770.11
780.00482
790.162
80.0963
800.722
810.549
820.175
830.458
840.94
850.042
860.24
870.0514
880.546
890.358
90.379
900.426
910.366
920.129
930.645
940.132
950.0168
960.816
970.816
980.174
990.669



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: CNhs12726


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)
0000031 (neuroblast)
0000034 (stem cell)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000393 (electrically responsive cell)
0000404 (electrically signaling cell)
0000540 (neuron)
0000548 (animal cell)
0000723 (somatic stem cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)

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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