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FF:11864-125B1: 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 17:32, 29 March 2012


Name:CD14+ monocytes - treated with Group A streptococci, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexfemale
age69
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD3-5
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-Peripheral1.101
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
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C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
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-Whole0.283
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: CNhs13469

Jaspar motifP-value
MA0002.22.71172e-8
MA0003.10.757
MA0004.10.462
MA0006.11
MA0007.10.654
MA0009.10.496
MA0014.10.877
MA0017.10.189
MA0018.20.0772
MA0019.10.525
MA0024.10.00563
MA0025.10.00446
MA0027.10.849
MA0028.10.105
MA0029.10.129
MA0030.10.117
MA0031.10.251
MA0035.20.247
MA0038.10.427
MA0039.20.549
MA0040.10.636
MA0041.10.931
MA0042.10.607
MA0043.11.59199e-7
MA0046.10.00878
MA0047.20.195
MA0048.10.538
MA0050.13.03224e-15
MA0051.13.52811e-8
MA0052.10.0542
MA0055.10.431
MA0057.10.442
MA0058.10.279
MA0059.10.203
MA0060.13.12799e-10
MA0061.18.18623e-14
MA0062.20.959
MA0065.20.0341
MA0066.10.0222
MA0067.13.4348e-5
MA0068.10.621
MA0069.10.834
MA0070.10.0225
MA0071.10.384
MA0072.10.628
MA0073.10.426
MA0074.10.108
MA0076.10.112
MA0077.10.277
MA0078.10.381
MA0079.20.128
MA0080.23.80264e-11
MA0081.14.86425e-4
MA0083.10.749
MA0084.10.548
MA0087.10.987
MA0088.10.48
MA0090.10.499
MA0091.10.592
MA0092.10.28
MA0093.10.524
MA0099.28.47942e-44
MA0100.10.822
MA0101.16.1752e-16
MA0102.23.78027e-9
MA0103.10.0682
MA0104.20.563
MA0105.14.08935e-18
MA0106.10.815
MA0107.18.63178e-20
MA0108.20.279
MA0111.10.397
MA0112.22.2103e-4
MA0113.10.819
MA0114.10.24
MA0115.10.795
MA0116.12.21837e-4
MA0117.10.0738
MA0119.10.141
MA0122.10.826
MA0124.10.574
MA0125.10.203
MA0131.10.389
MA0135.10.232
MA0136.12.9648e-11
MA0137.20.283
MA0138.20.472
MA0139.10.794
MA0140.10.294
MA0141.10.143
MA0142.10.706
MA0143.10.968
MA0144.10.107
MA0145.10.564
MA0146.10.481
MA0147.10.615
MA0148.10.541
MA0149.10.224
MA0150.17.36638e-19
MA0152.10.698
MA0153.10.00101
MA0154.13.36551e-4
MA0155.10.937
MA0156.11.67345e-7
MA0157.10.738
MA0159.10.0335
MA0160.10.0963
MA0162.10.712
MA0163.12.94002e-8
MA0164.10.641
MA0258.10.0138
MA0259.10.722



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: CNhs13469

Novel motifP-value
10.094
100.0233
1000.988
1010.793
1020.914
1030.253
1040.523
1050.128
1069.54512e-4
1070.178
1080.678
1090.332
110.127
1100.181
1110.0625
1120.296
1130.473
1140.0208
1150.28
1160.86
1170.0709
1180.176
1190.143
120.356
1200.77
1210.618
1220.709
1230.304
1240.503
1250.199
1260.255
1270.513
1280.0463
1290.329
130.098
1300.258
1310.902
1320.0933
1330.496
1340.436
1350.928
1360.879
1370.0512
1380.349
1390.0611
140.534
1400.49
1410.277
1420.031
1430.0179
1440.508
1450.256
1460.827
1470.894
1480.0138
1490.858
150.146
1500.375
1510.397
1520.327
1530.549
1540.694
1550.889
1560.947
1570.521
1580.0697
1590.16
160.318
1600.35
1610.428
1620.275
1630.0981
1640.0918
1650.292
1660.778
1670.25
1680.174
1690.0125
170.22
180.0818
190.448
20.53
200.167
210.756
220.334
230.0322
240.482
250.531
260.0465
270.521
280.41
290.244
30.111
300.407
310.756
320.642
330.251
340.776
350.108
360.0526
370.0786
380.362
390.745
40.833
400.18
410.0252
420.332
430.0208
440.634
450.836
460.17
470.478
480.451
490.116
50.311
500.988
510.473
520.399
530.614
540.421
550.462
560.631
570.831
580.168
590.217
60.818
600.051
610.722
620.083
630.469
640.445
650.201
660.196
670.469
680.808
690.358
70.266
700.0523
710.0235
720.142
730.214
740.0318
750.129
760.148
770.502
780.0938
790.86
80.319
800.225
810.313
820.129
830.0306
840.0904
850.029
860.0825
870.537
880.803
890.213
90.323
900.102
910.392
920.278
930.527
940.0858
950.39
960.352
970.552
980.0996
990.0894



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: CNhs13469


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)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000860 (classical monocyte)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002057 (CD14-positive, CD16-negative classical monocyte)
0002087 (nongranular leukocyte)
0002194 (monopoietic 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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