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FF:11884-125D3: Difference between revisions

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|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:34, 29 March 2012


Name:CD14+ monocytes - treated with Group A streptococci, donor3
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
age21
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD5-5
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-Peripheral1.074
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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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-Whole0.358
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: CNhs13492

Jaspar motifP-value
MA0002.29.0201e-9
MA0003.10.76
MA0004.10.274
MA0006.10.846
MA0007.10.723
MA0009.10.459
MA0014.10.818
MA0017.10.203
MA0018.20.0192
MA0019.10.611
MA0024.10.0057
MA0025.15.06774e-4
MA0027.10.913
MA0028.10.0977
MA0029.10.155
MA0030.10.21
MA0031.10.318
MA0035.20.291
MA0038.10.608
MA0039.20.588
MA0040.10.637
MA0041.10.632
MA0042.10.898
MA0043.14.45216e-9
MA0046.10.00609
MA0047.20.275
MA0048.10.556
MA0050.14.59005e-13
MA0051.12.61777e-6
MA0052.10.0231
MA0055.10.405
MA0057.10.378
MA0058.10.111
MA0059.10.142
MA0060.19.54845e-9
MA0061.12.38337e-15
MA0062.20.833
MA0065.20.0434
MA0066.10.0225
MA0067.13.83896e-6
MA0068.10.577
MA0069.10.964
MA0070.10.0302
MA0071.10.381
MA0072.10.535
MA0073.10.447
MA0074.10.101
MA0076.10.133
MA0077.10.277
MA0078.10.429
MA0079.20.147
MA0080.23.55867e-11
MA0081.14.99422e-4
MA0083.10.681
MA0084.10.89
MA0087.10.781
MA0088.10.487
MA0090.10.438
MA0091.10.68
MA0092.10.342
MA0093.10.306
MA0099.25.92922e-43
MA0100.10.78
MA0101.15.13168e-18
MA0102.24.16404e-9
MA0103.10.0543
MA0104.20.304
MA0105.12.29692e-20
MA0106.10.809
MA0107.12.67864e-22
MA0108.20.678
MA0111.10.395
MA0112.23.74735e-4
MA0113.10.978
MA0114.10.231
MA0115.10.722
MA0116.13.03006e-4
MA0117.10.0454
MA0119.10.144
MA0122.10.716
MA0124.10.448
MA0125.10.18
MA0131.10.423
MA0135.10.35
MA0136.16.14602e-12
MA0137.20.264
MA0138.20.31
MA0139.10.757
MA0140.10.323
MA0141.10.138
MA0142.10.821
MA0143.10.916
MA0144.10.128
MA0145.10.684
MA0146.10.562
MA0147.10.368
MA0148.10.662
MA0149.10.214
MA0150.15.65606e-19
MA0152.10.806
MA0153.10.00197
MA0154.11.65244e-4
MA0155.10.95
MA0156.16.2198e-8
MA0157.10.834
MA0159.10.0359
MA0160.10.0676
MA0162.10.97
MA0163.15.5256e-8
MA0164.10.69
MA0258.10.0247
MA0259.10.81



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: CNhs13492

Novel motifP-value
10.116
100.0209
1000.926
1010.766
1020.943
1030.296
1040.49
1050.124
1067.01329e-4
1070.23
1080.665
1090.37
110.193
1100.214
1110.0645
1120.289
1130.491
1140.0182
1150.267
1160.99
1170.0838
1180.191
1190.148
120.342
1200.769
1210.583
1220.643
1230.474
1240.538
1250.254
1260.26
1270.546
1280.0458
1290.346
130.0755
1300.307
1310.989
1320.0776
1330.693
1340.531
1350.867
1360.907
1370.0392
1380.414
1390.0748
140.571
1400.631
1410.263
1420.0591
1430.0235
1440.487
1450.404
1460.792
1470.838
1480.0191
1490.924
150.153
1500.328
1510.463
1520.348
1530.556
1540.757
1550.923
1560.755
1570.527
1580.0393
1590.127
160.362
1600.516
1610.37
1620.181
1630.182
1640.112
1650.288
1660.7
1670.208
1680.191
1690.0185
170.232
180.0821
190.529
20.471
200.16
210.802
220.353
230.0374
240.512
250.498
260.0709
270.446
280.364
290.265
30.168
300.425
310.761
320.411
330.265
340.845
350.1
360.0484
370.0674
380.378
390.796
40.845
400.191
410.0232
420.371
430.0213
440.584
450.864
460.231
470.629
480.558
490.118
50.297
500.984
510.511
520.395
530.688
540.498
550.655
560.71
570.906
580.17
590.252
60.857
600.0488
610.623
620.0962
630.51
640.466
650.234
660.226
670.474
680.68
690.475
70.238
700.0551
710.0266
720.16
730.2
740.0638
750.101
760.149
770.593
780.124
790.576
80.38
800.182
810.351
820.255
830.0249
840.116
850.0312
860.0516
870.567
880.797
890.293
90.36
900.136
910.335
920.322
930.497
940.0864
950.523
960.359
970.52
980.109
990.0508



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: CNhs13492


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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