Folks I've built an oncology query language (OQL), which enables cancer researchers to refine queries of cancer profile data (genetic status as a function of patient and gene). We call it an advanced gene filter <http://www.cbioportal.org/cgx/onco_spec_lang_desc.jsp>. In particular, researchers can use OQL to define genetic alterations, and thereby better investigate which genes are involved in which cancerous activities.
It supports multiple genomic datatypes (expression, copy number and mutation), discrete and continuous thresholds for alteration, nicknames, and arbitrary ordering of datatypes in the query. It also provides extensive error-checking. In one genetically detailed example, given what is known about the RB pathway, the events that are most likely selected for in the tumors are CCNE1 amplification, RB1 deletions or mutations, and loss of expression of CDKN2A. To investigate this hypothesis, we use this OQL: CCNE1: AMP MUTATED RB1: HOMDEL MUTATED CDKN2A: HOMDEL EXP < -1 to display only these events <http://www.cbioportal.org/cgx/index.do?cancer_type_id=ova&action=Submit&genetic_profile_ids=ova_mutations_next_gen&genetic_profile_ids=ova_gistic&genetic_profile_ids=ova_mrna_median_Zscores&MRNA_PROFILES_SELECTED=on&case_set_id=ova_4way_complete&Z_SCORE_THRESHOLD=1.0&case_ids=&gene_list=%0D%0ACCNE1%3A+AMP+MUTATED%3B%0D%0ARB1%3A+HOMDEL+MUTATED%3B%0D%0ACDKN2A%3A+HOMDEL+EXP+%3C+-1%0D%0A&tab_index=tab_visualize&gene_set_choice=user-defined_list&;>. BR A PS. It would be handy if the [email protected] account on [email protected] could be made to work. -- Senior Research Scientist Computational Biology Memorial Sloan-Kettering Cancer Center cBio Cancer Genomics Portal <http://www.cbioportal.org/> -- Arthur Goldberg www.cs.nyu.edu/artg We moved on Dec. 11. Our new address is 2741 Arlington Ave. Bronx NY 10463 List: http://www.antlr.org/mailman/listinfo/antlr-interest Unsubscribe: http://www.antlr.org/mailman/options/antlr-interest/your-email-address -- You received this message because you are subscribed to the Google Groups "il-antlr-interest" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/il-antlr-interest?hl=en.
