Website Tutorial: Examples of Functional Genomics Study search strategies
Last revision: February 9, 2012 by Elisabetta Manduchi, Emily Greenfest-Allen, Chris Stoeckert
Contact us with any comments, suggestions, or corrections for this tutorial.
The links below will take you to the GBCO Search Strategies page, importing the example strategies into your search strategy workbench.
| Strategy name | Example of | Description |
| Genes co-located with predicted Sox17 binding sites | Simple Genomic Co-location Strategy | Find all DNA sequence matches to a binding motif for Sox17 in a region of interest and then use genomic co-location to identify known protein-coding genes containing matched sequences. |
Genomic colocation tutorial Video
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Genomic Co-location strategy |
Find mouse genes on chromosome 6 whose proximal promoter overlaps with a consensus motif for Ptf1. (opens new window or tab) |
| Studies on Endocrine Pancreas Development and Growth | Simple Strategy | Find all studies on pancreas development and growth that focus on endocrine cells by intersecting the results of two queries. |
| Studies on Endocrine Pancreas Development and Growth, including Cell Lines | Nested Strategy | Find studies on pancreas development and growth that focus on endocrine cells or cell lines by intersecting the results from a query and a (nested) strategy that uses a union to identify all studies that are associated with endocrine cells or related cell lines. |
| TFs predicted to be Ptf1 targets in Pancreatic Endoderm | Simple Strategy | Find all trancription factors that have been predicted to be Ptf1 targets in murine pancreatic endoderm by intersecting the results of three queries. |
| TFs predicted to be Ptf1 targets in Pancreatic Endoderm, identified using Weights | Strategy using Weighted Unions | Find all trancription factors that have been predicted to be Ptf1 targets in murine pancreatic endoderm by determining the union of three weighted queries and ranking results according to their weight. Top-ranked results match all query criteria. |
| TFs expressed in Pancreatic Endoderm that are potential Ptf1a Targets | Nested Strategy | Find all transcription factors expressed in murine pancreatic endoderm that are potential Ptf1a targets by intersecting the results of two queries and a nested strategy that identifies potential Ptf1a targets based on predicted binding sites in the promoter or ChIP evidence for Ptf1a binding in the adult pancreas. |
| TFs expressed in Pancreatic Endoderm that are potential Ptf1a Targets, with lower emphasis on in silico predictions | Nested Strategy using Weighted Unions | Find all transcription factors expressed in murine pancreatic endoderm that are potential Ptf1a targets by intersecting the results of two queries and a nested strategy that identifies potential Ptf1a targets based on predicted binding sites in the promoter or ChIP evidence for Ptf1a binding in the adult pancreas. Rank results within the nested strategy, giving ChIP evidence a higher weight. |
| Gene-Gene Interactions in Beta or Beta-like cells that do not involve Pdx1 | Nested Strategy using Minus Operator and Filters | Use a union to find all curated, experimentally, or computationally inferred relationships associated with beta (insulin+ cells) or beta-like (cell lines or transdifferentiated cells). As a nested strategy, combine these resultswith the local gene neighborhood of Pdx1 using the minus operator to remove all relationships involving Pdx1. Filter the result to view only gene-gene interactions. |
