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Big Cell Line Association Miner

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tursynay edited this page Dec 13, 2023 · 2 revisions

Description: Big GIM stands for Gene Interaction Miner. Big GIM is a set of Google BigQuery tables that contain interaction data for pairs of genes in 4 areas:

  1. tissue-specific gene expression correlations from healthy tissue (GTEx)
  2. tissue-specific gene expression correlations from cancer samples (TCGA)
  3. tissue-specific probabilities of function interaction (GIANT)
  4. direct gene interactions (BioGRID)

1 and 2 were computed using Spearman rank correlation using MATLAB for all pairs of genes in the data where the coefficient of variation of the expression of both genes was at least 0.05, the number of samples with gene expression values greater than 0 is at least 5, there are at least 25 samples with expression values for both genes.

BigGIM_70 = R value of .7 to be kept BigGIM_80 = R value of .8 to be kept BigGIM_90 = R value of .9 to be kept

Example edge:

Additional Links: github.com/PriceLab/translator-bigquery-api

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Knowledge Providers (KP)

Autonomous Relay Agents (ARA)

Autonomous Relay System (ARS)

Standards and Reference Implementation (SRI)

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