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FF:11565-120D8: 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, donor2
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 stage50 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-S
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-Natural0.425
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0404
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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: CNhs12594

Jaspar motifP-value
MA0002.20.00108
MA0003.10.279
MA0004.10.79
MA0006.10.565
MA0007.10.497
MA0009.10.0574
MA0014.10.861
MA0017.10.0345
MA0018.25.92501e-11
MA0019.10.152
MA0024.10.176
MA0025.10.0019
MA0027.10.575
MA0028.10.597
MA0029.10.00147
MA0030.11.28185e-4
MA0031.10.0906
MA0035.26.49565e-9
MA0038.10.0318
MA0039.20.0317
MA0040.10.749
MA0041.10.166
MA0042.10.178
MA0043.11.08164e-6
MA0046.10.633
MA0047.20.53
MA0048.10.722
MA0050.10.776
MA0051.10.532
MA0052.11.29862e-4
MA0055.10.524
MA0057.10.308
MA0058.10.318
MA0059.10.183
MA0060.10.881
MA0061.13.16467e-20
MA0062.22.72384e-6
MA0065.20.053
MA0066.10.566
MA0067.11.99628e-9
MA0068.10.00247
MA0069.10.921
MA0070.10.119
MA0071.10.7
MA0072.10.425
MA0073.10.133
MA0074.10.5
MA0076.10.342
MA0077.10.302
MA0078.10.761
MA0079.20.00803
MA0080.23.79692e-12
MA0081.13.89135e-4
MA0083.10.234
MA0084.10.513
MA0087.10.921
MA0088.10.00155
MA0090.10.00136
MA0091.10.465
MA0092.10.537
MA0093.10.783
MA0099.21.1048e-17
MA0100.10.69
MA0101.17.95119e-18
MA0102.20.375
MA0103.10.00195
MA0104.20.469
MA0105.11.40561e-7
MA0106.10.022
MA0107.15.37822e-20
MA0108.25.45448e-6
MA0111.10.32
MA0112.20.745
MA0113.10.723
MA0114.10.0265
MA0115.10.529
MA0116.10.0529
MA0117.10.00127
MA0119.10.106
MA0122.10.581
MA0124.10.776
MA0125.10.266
MA0131.10.239
MA0135.10.102
MA0136.17.22046e-12
MA0137.20.696
MA0138.20.616
MA0139.10.405
MA0140.14.49023e-7
MA0141.10.147
MA0142.10.178
MA0143.10.494
MA0144.10.711
MA0145.10.425
MA0146.10.108
MA0147.10.134
MA0148.10.396
MA0149.10.706
MA0150.12.3895e-4
MA0152.10.116
MA0153.10.158
MA0154.10.437
MA0155.10.537
MA0156.19.32669e-6
MA0157.10.973
MA0159.10.494
MA0160.10.223
MA0162.10.0117
MA0163.10.141
MA0164.10.61
MA0258.10.944
MA0259.10.511



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: CNhs12594

Novel motifP-value
10.191
100.395
1000.203
1010.421
1020.807
1030.405
1040.859
1050.228
1060.318
1070.0331
1080.156
1090.868
110.42
1100.269
1110.191
1120.731
1130.505
1140.127
1150.717
1160.0922
1170.0898
1180.322
1190.164
120.604
1200.0462
1210.153
1220.243
1230.256
1240.0247
1250.249
1260.295
1270.771
1280.774
1290.0125
130.462
1300.51
1310.943
1320.0623
1330.0883
1340.438
1350.792
1360.175
1370.0446
1380.256
1390.838
140.66
1400.241
1410.225
1420.139
1430.86
1440.997
1450.411
1460.318
1470.134
1480.737
1490.0858
150.637
1500.706
1510.495
1520.0305
1530.551
1540.849
1550.209
1560.826
1570.934
1580.185
1590.828
160.211
1600.0642
1610.448
1620.0663
1630.115
1640.432
1650.767
1660.021
1670.411
1680.312
1690.851
170.647
180.32
190.298
20.118
200.377
210.741
220.604
230.78
240.928
250.885
260.519
270.264
280.613
290.412
30.249
300.473
310.462
320.00582
330.825
340.835
350.175
360.893
370.47
380.77
390.717
40.641
400.647
410.372
420.248
430.467
440.111
450.757
460.418
470.319
480.208
490.498
50.779
500.921
510.968
520.905
530.961
540.951
550.65
560.53
570.0981
580.657
590.818
60.647
600.867
610.638
620.934
630.301
640.47
650.629
660.789
670.619
680.756
690.202
70.814
700.308
710.516
720.287
730.111
740.0125
750.738
760.878
770.0681
780.914
790.4
80.103
800.393
810.293
820.812
830.939
840.269
850.841
860.0741
870.471
880.53
890.0593
90.649
900.321
911
920.521
930.583
940.957
950.0966
960.455
970.79
980.496
994.37843e-5



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: CNhs12594


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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