Abstract 2469: The COSMIC Cancer Gene Census - a comprehensive study of all mutated cancer-driving genes

AbstractUnderstanding a mutation in cancer requires knowledge of the different roles that genes play in cancer as drivers, oncogenes and tumor suppressors. We present CancerMine, a high-quality text-mined knowledgebase that catalogues over 856 genes as drivers, 2,421 as oncogenes and 2,037 as tumor suppressors in 426 cancer types. We compile 3,485 genes that are not in the IntOGen resource of drivers and complement the Cancer Gene Census with 3,136 new genes identified as oncogenes and tumor suppressors. CancerMine provides a method for gene-centric clustering of cancer types illustrating genetic similarities between cancer types of different organs and was validated against data from the Cancer Genome Atlas (TCGA) project. Finally with 178 novel cancer gene mentions in publications each month, this resource will be updated monthly, pre-empting the need to manually curate the ever-increasing number of novel cancer associated genes. CancerMine is viewable through a web portal (http://bionlp.bcgsc.ca/cancermine/) and available for download (https://github.com/jakelever/cancermine).

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In silico prediction of tumor antigens derived from functional missense mutations of the cancer gene census

OncoImmunology ◽

10.4161/onci.21511 ◽

2012 ◽

Vol 1 (8) ◽

pp. 1281-1289 ◽

Cited By ~ 16

Author(s):

Jahan S. Khalili ◽

Russell W. Hanson ◽

Zoltan Szallasi

Keyword(s):

In Silico ◽

Tumor Antigens ◽

Missense Mutations ◽

Cancer Gene ◽

In Silico Prediction ◽

Cancer Gene Census

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Cancer Gene Census (CGC)

Dictionary of Bioinformatics and Computational Biology ◽

10.1002/9780471650126.dob0833 ◽

2004 ◽

Author(s):

Malachi Griffith ◽

Obi L. Griffith

Keyword(s):

Cancer Gene ◽

Cancer Gene Census

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Progress In The Practical Application Of Automated Image Analysis To Tem Negatives

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100078614 ◽

1977 ◽

Vol 35 ◽

pp. 214-217

Author(s):

F. A. Heckman ◽

E. Redman ◽

J.E. Connolly

Keyword(s):

Image Analysis ◽

Image Quality ◽

Exposure Time ◽

Image Contrast ◽

Automated Image Analysis ◽

Practical Application ◽

Factors Affecting ◽

High Image Quality ◽

Qualitative Evidence ◽

Comprehensive Study

In our initial publication on this subject1) we reported results demonstrating that contrast is the most important factor in producing the high image quality required for reliable image analysis. We also listed the factors which enhance contrast in order of the experimentally determined magnitude of their effect. The two most powerful factors affecting image contrast attainable with sheet film are beam intensity and KV. At that time we had only qualitative evidence for the ranking of enhancing factors. Later we carried out the densitometric measurements which led to the results outlined below.Meaningful evaluations of the cause-effect relationships among the considerable number of variables in preparing EM negatives depend on doing things in a systematic way, varying only one parameter at a time. Unless otherwise noted, we adhered to the following procedure evolved during our comprehensive study:Philips EM-300; 30μ objective aperature; magnification 7000- 12000X, exposure time 1 second, anti-contamination device operating.

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Hexachlorobenzene toxicity in the monkey ovary: III. Ultrastructure induced by high (10 mg/kg) dose exposure

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100084958 ◽

1991 ◽

Vol 49 ◽

pp. 130-131

Author(s):

A. Singh ◽

A. Dykeman ◽

J. Jarrelf ◽

D. C. Villeneuve

Keyword(s):

Present Report ◽

Reproductive Toxicity ◽

Control Group ◽

Primate Model ◽

Human Follicular Fluid ◽

Thin Sections ◽

Cynomolgus Monkeys ◽

Cacodylate Buffer ◽

Induction Cycle ◽

Comprehensive Study

Hexachlorobenzene (HCB), a persistent and mobile organochlorine pesticide, occurs in environment. HCB has been shown to be present in human follicular fluid. An objective of the present report, which is part of a comprehensive study on reproductive toxicity of HCB, was to determine the cytologic effects of the compound on ovarian follicles in a primate model.Materials and Methods. Eight Cynomolgus monkeys were housed under controlled conditions at Animal facility of Health and Welfare, Ottawa. Animals were orally administered gelatin capsules containing HCB mixed with glucose in daily dosages of 0.0 or 10 mg/kg b.w. for 90 days; the former was the control group. On the menstrual period following completion of dosing, the monkeys underwent an induction cycle of superovulation. At necropsy, one-half of an ovary from each animal was diced into ca. 2- to 3-mm cubed specimens that were fixed by immersion in 2.5% glutaraldehyde in 0.1 M cacodylate buffer (pH 7.3). Subsequent procedures followed to obtain thin sections that were examined in a Hitachi H-7000 electron microscope have been described earlier.

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Comparison of Substructures Between Uniaxial and Biaxial Deformation in 1100-0 Aluminum

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100096989 ◽

1981 ◽

Vol 39 ◽

pp. 52-53

Author(s):

D. L. Rohr ◽

S. S. Hecker

Keyword(s):

Plastic Strain ◽

Cell Walls ◽

Room Temperature ◽

Mechanical Response ◽

Biaxial Tension ◽

Initial Deformation ◽

Uniaxial Deformation ◽

Biaxial Deformation ◽

Stress States ◽

Comprehensive Study

As part of a comprehensive study of microstructural and mechanical response of metals to uniaxial and biaxial deformations, the development of substructure in 1100 A1 has been studied over a range of plastic strain for two stress states.Specimens of 1100 aluminum annealed at 350 C were tested in uniaxial (UT) and balanced biaxial tension (BBT) at room temperature to different strain levels. The biaxial specimens were produced by the in-plane punch stretching technique. Areas of known strain levels were prepared for TEM by lapping followed by jet electropolishing. All specimens were examined in a JEOL 200B run at 150 and 200 kV within 24 to 36 hours after testing.The development of the substructure with deformation is shown in Fig. 1 for both stress states. Initial deformation produces dislocation tangles, which form cell walls by 10% uniaxial deformation, and start to recover to form subgrains by 25%. The results of several hundred measurements of cell/subgrain sizes by a linear intercept technique are presented in Table I.

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