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FF:11566-120D9: 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 17:23, 29 March 2012


Name:Mast cell, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stage41 years old adult
sexfemale
age76
cell typemast cell
cell lineNA
companyNA
collaborationSven Guhl (Charite Germany)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberBsMC-T
catalog numberNA
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
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-Natural0.899
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0119
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0585
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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: CNhs12593

Jaspar motifP-value
MA0002.20.0329
MA0003.10.525
MA0004.10.83
MA0006.10.92
MA0007.10.18
MA0009.10.117
MA0014.10.855
MA0017.10.0376
MA0018.22.05499e-10
MA0019.10.282
MA0024.10.629
MA0025.17.46114e-4
MA0027.10.939
MA0028.10.109
MA0029.10.0124
MA0030.18.5122e-5
MA0031.10.0328
MA0035.21.87395e-7
MA0038.10.00942
MA0039.20.112
MA0040.10.57
MA0041.10.463
MA0042.10.169
MA0043.11.96753e-7
MA0046.10.793
MA0047.20.267
MA0048.10.554
MA0050.10.573
MA0051.10.779
MA0052.10.00813
MA0055.10.46
MA0057.10.191
MA0058.10.98
MA0059.10.0228
MA0060.10.612
MA0061.11.54939e-11
MA0062.26.92424e-7
MA0065.20.0502
MA0066.10.197
MA0067.15.94452e-8
MA0068.14.79623e-4
MA0069.10.886
MA0070.10.424
MA0071.10.417
MA0072.10.495
MA0073.10.377
MA0074.10.682
MA0076.10.0835
MA0077.10.312
MA0078.10.705
MA0079.20.00663
MA0080.23.08809e-12
MA0081.13.82155e-4
MA0083.10.658
MA0084.10.518
MA0087.10.76
MA0088.10.0146
MA0090.10.00248
MA0091.10.424
MA0092.10.377
MA0093.10.823
MA0099.21.65572e-5
MA0100.10.36
MA0101.18.97473e-13
MA0102.20.247
MA0103.10.0019
MA0104.20.0598
MA0105.11.9162e-4
MA0106.10.0111
MA0107.13.17301e-13
MA0108.20.0524
MA0111.10.378
MA0112.20.153
MA0113.10.0815
MA0114.10.0279
MA0115.10.832
MA0116.10.0397
MA0117.10.0219
MA0119.10.0238
MA0122.10.421
MA0124.10.687
MA0125.10.189
MA0131.10.0626
MA0135.10.284
MA0136.12.63305e-12
MA0137.20.0871
MA0138.20.744
MA0139.10.677
MA0140.15.81731e-5
MA0141.10.0549
MA0142.10.127
MA0143.10.731
MA0144.10.243
MA0145.10.768
MA0146.10.184
MA0147.10.00612
MA0148.10.418
MA0149.10.453
MA0150.10.0981
MA0152.10.106
MA0153.10.244
MA0154.10.913
MA0155.10.98
MA0156.14.17578e-6
MA0157.10.672
MA0159.10.256
MA0160.10.425
MA0162.10.0261
MA0163.10.393
MA0164.10.689
MA0258.10.631
MA0259.10.335



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: CNhs12593

Novel motifP-value
10.0849
100.344
1000.241
1010.753
1020.835
1030.319
1040.923
1050.618
1060.797
1070.0173
1080.108
1090.855
110.299
1100.146
1110.144
1120.92
1130.65
1140.0869
1150.811
1160.17
1170.0829
1180.3
1190.0981
120.602
1200.254
1210.284
1220.506
1230.514
1240.0565
1250.273
1260.637
1270.601
1280.749
1290.0022
130.739
1300.447
1310.696
1320.151
1330.0599
1340.426
1350.683
1360.0422
1370.0396
1380.287
1390.67
140.805
1400.182
1410.175
1420.0351
1430.729
1440.874
1450.593
1460.325
1470.137
1480.695
1490.0896
150.474
1500.939
1510.393
1520.101
1530.665
1540.709
1550.204
1560.705
1570.512
1580.507
1590.289
160.199
1600.0508
1610.349
1620.147
1630.358
1640.412
1650.918
1660.0362
1670.328
1680.179
1690.352
170.411
180.144
190.306
20.106
200.43
210.559
220.931
230.842
240.647
250.855
260.303
270.248
280.626
290.427
30.317
300.477
310.34
320.00338
330.801
340.646
350.144
360.705
370.804
380.638
390.574
40.412
400.41
410.985
420.294
430.454
440.046
450.579
460.249
470.209
480.164
490.422
50.728
500.926
510.859
520.883
530.953
540.809
550.584
560.483
570.0871
580.79
590.666
60.78
600.818
610.56
620.749
630.246
640.356
650.339
660.766
670.229
680.521
690.164
70.769
700.383
710.389
720.416
730.402
740.00818
750.98
760.758
770.0512
780.449
790.294
80.0701
800.45
810.308
820.924
830.773
840.342
850.632
860.0642
870.332
880.446
890.0109
90.728
900.614
910.878
920.346
930.252
940.695
950.0629
960.301
970.717
980.414
991.14993e-4



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: CNhs12593


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)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000097 (mast cell)
0000134 (mesenchymal cell)
0000151 (secretory cell)
0000163 (endocrine cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000457 (biogenic amine secreting cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000831 (mast cell progenitor)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002028 (basophil mast progenitor cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002191 (granulocytopoietic cell)
0002274 (histamine secreting cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
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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