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FF:11885-125D4: 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 17:37, 29 March 2012


Name:CD14+ monocytes - treated with lipopolysaccharide, 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 numberD5-6
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-Peripheral0.95
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-Whole0.213
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: CNhs13545

Jaspar motifP-value
MA0002.21.12092e-7
MA0003.10.792
MA0004.10.421
MA0006.10.971
MA0007.10.874
MA0009.10.618
MA0014.10.694
MA0017.10.214
MA0018.20.171
MA0019.10.577
MA0024.10.0103
MA0025.10.00111
MA0027.10.924
MA0028.10.268
MA0029.10.102
MA0030.10.194
MA0031.10.324
MA0035.20.291
MA0038.10.779
MA0039.20.952
MA0040.10.537
MA0041.10.331
MA0042.10.896
MA0043.17.5311e-9
MA0046.10.0125
MA0047.20.336
MA0048.10.518
MA0050.12.43811e-17
MA0051.13.25306e-12
MA0052.10.227
MA0055.10.394
MA0057.10.424
MA0058.10.231
MA0059.10.172
MA0060.12.71443e-7
MA0061.12.59844e-19
MA0062.20.393
MA0065.20.0312
MA0066.10.0445
MA0067.12.56984e-5
MA0068.10.679
MA0069.10.803
MA0070.10.0168
MA0071.10.589
MA0072.10.611
MA0073.10.468
MA0074.10.145
MA0076.10.255
MA0077.10.271
MA0078.10.651
MA0079.20.159
MA0080.22.33178e-11
MA0081.15.93178e-4
MA0083.10.522
MA0084.10.687
MA0087.10.806
MA0088.10.722
MA0090.10.378
MA0091.10.861
MA0092.10.338
MA0093.10.454
MA0099.28.88674e-41
MA0100.10.894
MA0101.15.93033e-24
MA0102.21.15461e-9
MA0103.10.0339
MA0104.20.343
MA0105.15.29727e-22
MA0106.10.867
MA0107.12.10004e-30
MA0108.20.61
MA0111.10.468
MA0112.24.83706e-4
MA0113.10.738
MA0114.10.19
MA0115.10.874
MA0116.12.34836e-4
MA0117.10.0629
MA0119.10.132
MA0122.10.494
MA0124.10.321
MA0125.10.204
MA0131.10.528
MA0135.10.29
MA0136.11.2276e-12
MA0137.20.0106
MA0138.20.226
MA0139.10.966
MA0140.10.455
MA0141.10.227
MA0142.10.637
MA0143.10.958
MA0144.10.0206
MA0145.10.543
MA0146.10.57
MA0147.10.437
MA0148.10.775
MA0149.10.244
MA0150.13.89021e-21
MA0152.10.917
MA0153.10.00251
MA0154.12.22767e-4
MA0155.10.976
MA0156.12.54418e-9
MA0157.10.986
MA0159.10.0365
MA0160.10.138
MA0162.10.934
MA0163.19.94687e-9
MA0164.10.616
MA0258.10.0313
MA0259.10.748



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: CNhs13545

Novel motifP-value
10.0912
100.0236
1000.91
1010.982
1020.916
1030.216
1040.497
1050.179
1067.14567e-4
1070.236
1080.614
1090.299
110.149
1100.148
1110.113
1120.427
1130.429
1140.0317
1150.156
1160.885
1170.0846
1180.209
1190.124
120.297
1200.563
1210.773
1220.7
1230.611
1240.836
1250.168
1260.226
1270.577
1280.0706
1290.328
130.0827
1300.433
1310.917
1320.122
1330.878
1340.566
1350.756
1360.766
1370.0344
1380.506
1390.112
140.546
1400.601
1410.261
1420.235
1430.0315
1440.445
1450.299
1460.872
1470.869
1480.0108
1490.97
150.156
1500.31
1510.602
1520.541
1530.802
1540.795
1550.853
1560.7
1570.863
1580.0946
1590.0737
160.313
1600.404
1610.41
1620.253
1630.158
1640.168
1650.18
1660.999
1670.281
1680.0735
1690.0193
170.274
180.111
190.555
20.398
200.173
210.81
220.346
230.0393
240.384
250.418
260.0591
270.565
280.308
290.243
30.12
300.365
310.719
320.411
330.161
340.771
350.108
360.0594
370.065
380.397
390.782
40.921
400.192
410.0283
420.294
430.0198
440.537
450.75
460.187
470.501
480.477
490.153
50.296
500.947
510.56
520.349
530.67
540.482
550.62
560.697
570.835
580.185
590.247
60.747
600.04
610.729
620.0928
630.533
640.484
650.232
660.424
670.399
680.461
690.21
70.218
700.0435
710.0284
720.193
730.268
740.0454
750.146
760.171
770.563
780.122
790.693
80.337
800.158
810.289
820.203
830.033
840.0836
850.0517
860.0831
870.341
880.758
890.213
90.389
900.0838
910.437
920.27
930.489
940.0886
950.538
960.404
970.466
980.156
990.0948



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: CNhs13545


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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