Third-Party Tools

The following third-party tools are embedded into tranSMART Analyze:

Dalliance Genome Browser

The Dalliance Genome Browser allows you to visualize genomic data, compare genomic variants between different patient cohorts, compare different types of genomic information, and compare the data with public genomic information, such as COSMIC variations.

To view tranSMART data in the Genome Browser:

  1. In Analyze, open the study of interest, or open the Advanced Trials folder to run an analysis of data from multiple studies.
  2. Define your cohort(s) as described in Defining the Cohorts.
  3. Click the Genome Browser tab to display the data in the Genome Browser: image165
  4. Optionally, to add additional data from the study data, drag the concepts of interest from the study into the Genome Browser.

Quick Tour

Information about the Genome Browser is located here:

To see a description of a UI control, hover the mouse pointer over the control:

image166

Some highlights of the UI are shown below:

image167

Genomic Variants

If the study has a genomic variants concept, drag it into the browser for a visualization of variants such as SNPs, unidentified mutations, insertions, and deletions:

image168

Note that:

  • A green upward-pointing arrow represents an insertion.
  • A red downward-pointing arrow represents a deletion.
  • Clicking an icon displays details about the variant. Below, a blue plus-sign icon is clicked to display details about a SNP:

image169

MetaCore Enrichment Analysis

Enrichment analysis is one of the main approaches to understanding the biology behind genes or an expression profile, finding the most significant pathways and processes related to a studied phenotype, validating the relevance of a gene signature, and other use cases.

The enrichment analysis plug-in offered by Thomson Reuters for tranSMART includes options for publically available or the entire portfolio of MetaCore pathway maps, which can be further enhanced by Specialty Module pathway maps created for different diseases.

In the following figure, a histogram represents enrichment analysis results across MetaCore and disease pathway maps in the tranSMART interface.

image170

To perform a MetaCore Enrichment Analysis:

  1. Define a cohort as described in Defining the Cohorts.

  2. Click the MetaCore Enrichment Analysis tab:

    image171

  3. Drag a high-dimensional data node (image172) into the Variable Selection box.

  4. Click the High Dimensional Data button.

    The Compare Subsets-Pathway Selection dialog appears.

  5. Specify the platform and other filters for the analysis.

    For information, see High Dimensional Data.

  6. Either click Run Workflow to run the analysis now, or click Apply Selections to define more parameters for the analysis and continue with the steps below.

  7. Optionally, specify the z-score threshold for the data.

  8. Optionally, click MetaCore Settings to view your settings.

  9. Click Run to run the analysis.

MetaCore Enrichment Analysis Based on Marker Selection Data

The enrichment analysis feature complements the Marker Selection advanced workflow (see Marker Selection on page 64) by providing enrichment of a gene list generated by the workflow to evaluate the significance of the genes to the studied phenotype and/or patient cohort.

Configuration

MetaCore Enrichment Analysis is an additional grails plugin. It is attached to a project in BuildConfig.groovy :

plugins {
    ...
    if (!dm) {
        ...
        runtime ':transmart-metacore-plugin:1.2.2-SNAPSHOT'
        ...
    } else {
    ...
    }
}

For both free and MetaCore enrichments, you need to specify the following line in your ~/.grails/transmartApp/Config.groovy:

com.thomsonreuters.transmart.metacoreAnalyticsEnable = true

You don’t need any extra settings in order for free enrichment to work.

To use MetaCore’s account, create a special table that will store user preferences. Execute search_user_settings.sql under searchapp or system Oracle user or the appropriate script for PostgreSQL, otherwise you will not be able to use full enrichment functionality. You can find scripts for creating this table here:

For postgres (see postgres.sql).

--
-- Name: search_user_settings; Type: TABLE; Schema: searchapp; Owner: -
--
CREATE TABLE search_user_settings (
    id bigint NOT NULL,
    setting_name character varying(255) NOT NULL,
    user_id bigint NOT NULL,
    setting_value character varying(1024) NOT NULL);

--
-- Name: search_user_settings_pkey; Type: CONSTRAINT; Schema: searchapp; Owner: -
--
ALTER TABLE ONLY search_user_settings
    ADD CONSTRAINT search_user_settings_pkey PRIMARY KEY (id);

--
-- Name: search_user_settings_uk; Type: CONSTRAINT; Schema: searchapp; Owner: -
--
ALTER TABLE ONLY search_user_settings
    ADD CONSTRAINT search_user_settings_uk UNIQUE (user_id, setting_name, setting_value);

For oracle (see oracle.sql).

--
-- Type: TABLE; Owner: SEARCHAPP; Name: SEARCH_USER_SETTINGS
--
CREATE TABLE "SEARCHAPP"."SEARCH_USER_SETTINGS"
(   "ID" NUMBER NOT NULL ENABLE,
"USER_ID" NUMBER NOT NULL ENABLE,
"SETTING_NAME" VARCHAR2(255 BYTE) NOT NULL ENABLE,
"SETTING_VALUE" VARCHAR2(1024 BYTE) NOT NULL ENABLE,
CONSTRAINT "SEARCH_USER_SETTINGS_PKEY" PRIMARY KEY ("ID")
USING INDEX
TABLESPACE "INDX"  ENABLE,
CONSTRAINT "SEARCH_USER_SETTINGS_UK" UNIQUE ("USER_ID", "SETTING_NAME", "SETTING_VALUE")
USING INDEX
TABLESPACE "INDX"  ENABLE
) SEGMENT CREATION IMMEDIATE
TABLESPACE "TRANSMART" ;

If you want all users to use their personal MetaCore account, you don’t need to do anything else. If you want an ability to use a common account for enrichments (users will have a choice), specify the default MetaCore credentials in ~/.grails/transmartApp/Config.groovy:

com.thomsonreuters.transmart.metacoreURL = 'https://portal.genego.com'
com.thomsonreuters.transmart.metacoreDefaultLogin = 'metacore_login'
com.thomsonreuters.transmart.metacoreDefaultPassword = 'metacore_password'