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Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism

Rajesh Pandey1, Amit K Mandal2, Vineet Jha2 and Mitali Mukerji1*

Author Affiliations

1 Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR-IGIB), Mall Road, Delhi-110007, India

2 GN Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR-IGIB), Mall Road, Delhi-110007, India

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Genome Biology 2011, 12:R117  doi:10.1186/gb-2011-12-11-r117

Published: 23 November 2011

Additional files

Additional file 1:

Genes differentially expressed in response to heat shock stress. This file contains a list of genes differentially expressed in response to heat shock stress using Illumina BeadChip, analyzed using Beadstudio software.

Format: XLS Size: 325KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Positional conservation of HSF sites. This file contains the data for the positional preference of HSF sites within Alus in sense and antisense orientations.

Format: XLS Size: 62KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Biased HSF site distribution for Alu orientation in upstream and genic regions. This file contains HSF site distribution data for Alu and non-Alu sequences in the upstream and genic regions of differentially regulated genes.

Format: XLS Size: 1.1MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

HSF density for upstream and genic regions. This file contains per gene HSF site density for both Alu and non-Alu sequences in the upstream and genic regions.

Format: XLS Size: 740KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Correlation of HSF sites to antisense signals. This file contains the HSF sites positions relative to the antisense signal co-ordinates from the exon array for down-regulated genes.

Format: XLS Size: 491KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Gene Ontology analysis. This file contains the GO category analysis using DAVID for differentially regulated genes. The genes are binned on the basis of the presence of HSF sites exclusively in Alu regions or exclusively in non-Alu regions or in both regions.

Format: XLS Size: 20KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Genes with HSF sites only in Alu regions. This file contains a list of all the up-regulated genes where the HSF sites in the upstream region are present exclusively in Alu sequences.

Format: XLS Size: 38KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Primers used for validation. This file contains all the primers used for experimental validation of the inferences from genome-wide expression profiling and subsequent bio-informatics analysis.

Format: XLS Size: 63KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data