Metasearch Process for Transcription Targets

Transcription

1 Step 1 Select 'Genes' This is the primary interface for the Metasearch add on to Thomson Reuters (GeneGO) platform. Metasearch allows one to make complex queries for information extraction. This document will walk you through how to do that in order to curate out transcription factor downstream genes, ie what genes does my transcription factor of interest regulate? Metasearch Process for Transcription Targets Page 1

2 Step 2 Constrain to 'Human' We want to constrain to human as that is our model system. Can be a litttle less stringent and include the other species to but that would have to convert those genes back to human ids. Metasearch Process for Transcription Targets Page 2

3 Step 3 Select 'interact downstream with' We chose this filter as we want genes that are 'downstream' from our Transcription factor because we are interested in genes being regulated. The upstream selection would select those genes that regulate our transcription factor. Metasearch Process for Transcription Targets Page 3

4 Step 4 - Filters for 'interact with downstream with' relations to Transcription Factor 1. Select 'Human' and 'Human specific' to constrain relation to an observation made in human model system. 2. The effect of relation from Transcription factor to target gene. 3. For finding genes regulated by transcription factor two mechanism are appropriate: 'Transcription regulation' and 'Influence on expression' Definitions Effect 'Unspecified': Direct interaction between two proteins via an unknown mechanism or indirect interaction between two proteins via unknown intermediate signal protein. Mechanism Direct 'Transcription regualtion': A change in gene expression levels by altering transcription rates regulated by transcription factors that physically bind to specific regulatory sequences of target genes. One of the direct interaction mechanisms in MetaCore. Mechanism Indirect 'Influence on expression': In MetaCore, change in expression level of a gene (target gene) caused by a protein or compound. One of the indirect interaction mechanisms in MetaCore. Metasearch Process for Transcription Targets Page 4

5 One can chose different combinations of these filters. It is dependent on what is being looked for. For example, if one wants high confidence downstream targets that are inhibited by your transcription factor of interest one would chose 'human' 'human specific' 'Inhibition' 'Transcription regulation' Step 5 - Example of 'Human' 'Human specific' 'Activation' 'Transcription regulation' Note the 'use high trust interactions only' box. This is an annotation stringency filter to observations in Metacore database. I leave it checked by default. Metasearch Process for Transcription Targets Page 5

6 Step 6 Select 'Network Objects' for Transcription Factor selection. A network object is a convention in Metacore to represent molecular entities. It allows mapping of multiple genes to a network for visualization. For example, NFkB is a transcription factor but it consists of the partnering of a number of protein gene products that come together in various ways. NFkB network object would encompass all of those, rather than just RELA for example. Picking the network object will capture more specific information rather than single genes by themselves. Metasearch Process for Transcription Targets Page 6

7 Step 7 Constrain TF 'Network Object' to 'Human' 'Human specific only' Again, 'Human specific only' keeps data strictly for human. Metasearch Process for Transcription Targets Page 7

8 Step 8 Select your Transcription Factor 'Network Object' Search box has autocomplete fucntions for what you are searching for proper matching. Metasearch Process for Transcription Targets Page 8

9 Step 9 Final search screen Metasearch Process for Transcription Targets Page 9

10 Step 10 Search Result Screeen Metasearch Process for Transcription Targets Page 10

11 Step 11 Export 1. Hit this to bring up the Export dialog window. Metasearch Process for Transcription Targets Page 11

12 Step 12 Select Export Options 1. Select this to get query results as they appear in search result screen. 2. Make sure to select all rows, as there is usually more than one page of results. Metasearch Process for Transcription Targets Page 12

13 Step 13 Final Output File Metasearch Process for Transcription Targets Page 13