Open Access Highly Accessed Research article

Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the progression of polycystic kidney disease

Priyanka Pandey1, Shan Qin1, Jacqueline Ho2, Jing Zhou3 and Jordan A Kreidberg14*

Author Affiliations

1 Department of Medicine, Children's Hospital Boston; Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA

2 Current address: Division of Nephrology, Department of Pediatrics, University of Pittsburg School of Medicine, Pittsburg, PA, 15224, USA

3 Department of Medicine, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School. Boston, MA, 02115, USA

4 Harvard Stem Cell Institute, Cambridge, MA, 02138, USA

For all author emails, please log on.

BMC Systems Biology 2011, 5:56  doi:10.1186/1752-0509-5-56

Published: 25 April 2011

Additional files

Additional file 1:

Schematic representation of target miRNA prediction for significantly regulated genes. Step-wise approaches used to predict target miRNAs for the significantly regulated genes obtained at three comparisons, shown in Additional file 1. We used four prediction tools- TargetScan, miRanda, miRDB and microT and the results obtained from individual tool were overlapped by custom written Perl scripts. Only those miRNA-mRNA pairs were considered for further study that were predicted by atleast two tools.

Format: PDF Size: 213KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Perl script used for integrating prediction tools results. Perl script used for integrating prediction tools results

Format: PDF Size: 45KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Gene-primers used for qPCR. This table shows list of primers used for qPCR analysis of genes

Format: XLS Size: 34KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Design of experiment. This figure shows the experimental design implied in this study. It shows four comparisons including two stages-E14.5 and E17.5 and two genotypes- Pkd1-/- and wild-type.

Format: PDF Size: 152KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Significantly regulated genes at E14.5. This table shows the significantly regulated genes obtained for mutant versus wild-type comparison at E14.5

Format: XLS Size: 199KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Significantly regulated genes at E17.5. This table shows the significantly regulated genes obtained for mutant versus wild-type comparison at E17.5

Format: XLS Size: 403KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Significantly regulated genes in wild-types across time points E14.5 to E17.5. This table shows the significantly regulated genes obtained for wild-types when compared at E14.5 and E17.5

Format: XLS Size: 411KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Significantly regulated genes in mutants across time points E14.5 to E17.5. This table shows the significantly regulated genes obtained for mutant when compared at E14.5 and E17.5

Format: XLS Size: 782KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 9:

Significantly regulated genes specific for disease transition. This table shows the significantly regulated genes that are specific for transition under disease condition.

Format: XLS Size: 660KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 10:

Significantly regulated genes specific for healthy transition. This table shows the significantly regulated genes that are specific for transition under healthy condition.

Format: XLS Size: 161KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 11:

Significantly regulated genes specific to aging. This table shows the significantly regulated genes that are specific for aging and common to both diseased and healthy conditions.

Format: XLS Size: 515KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 12:

Gene Ontology terms- overrepresented biological processes. This table shows the overrepresented Biological Processes from Gene ontology for significantly regulated genes. Sheets 1 through 3 show overrepresented biological processes for up- and down-regulated genes obtained for E14.5 mutant versus wild-type comparison, E17.5 mutant versus wild-type, and mutants at E14.5 versus E17.5.

Format: XLS Size: 201KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 13:

Gene Set Enrichment Analysis- overrepresented gene sets or pathways. This table shows the overrepresented gene-sets/pathways obtained from Gene Set Enrichment Analysis for significantly regulated genes. Sheets 1 through 3 show overrepresented gene-sets for up- and down-regulated genes obtained for E14.5 mutant versus wild-type comparison, E17.5 mutant versus wild-type, and mutants at E14.5 versus E17.5.

Format: XLS Size: 60KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 14:

Common genes obtained between Pkd1L3/L3 and Pkd1-/- mouse models. This figure shows some of the early and late responsive genes we obtained in comparison between Pkd1L3/L3 and Pkd1-/- mouse models.

Format: PDF Size: 292KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 15:

Common genes in Pkd1L3/L3 and Pkd1-/- mouse models. This table shows the common genes and pathways obtained from comparing the Pkd1L3/L3 and Pkd1-/- mouse models.

Format: XLS Size: 165KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 16:

Common genes in Pkd1-/- mouse model and human ADPKD. This table shows the common genes and pathways obtained from comparing the Pkd1-/- mouse model and human ADPKD.

Format: XLS Size: 444KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 17:

Gene Set Enrichment Analysis- overrepresented gene sets with shared Transcription Factors. This table shows the overrepresented overrepresented gene sets with shared Transcription Factors obtained from Gene Set Enrichment Analysis for significantly regulated genes. Sheets 1 through 3 show overrepresented gene-sets with shared Transcription Factors for up- and down-regulated genes obtained for E14.5 mutant versus wild-type comparison, E17.5 mutant versus wild-type, and mutants at E14.5 versus E17.5.

Format: XLS Size: 52KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 18:

Predicted target miRNAs for significantly regulated genes at E14.5. This table shows the predicted target miRNAs for significantly regulated genes at E14.5. Four tools-TargetScan, miRanda, miRDB and microT were used for prediction and results were overlapped. Only those miRNA:gene pairs are shown that are predicted by atleast two tools.

Format: XLS Size: 601KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 19:

Predicted target miRNAs for significantly regulated genes at E17.5. This table shows the predicted target miRNAs for significantly regulated genes at E17.5. Four tools-TargetScan, miRanda, miRDB and microT were used for prediction and results were overlapped. Only those miRNA:gene pairs are shown that are predicted by atleast two tools.

Format: XLS Size: 1.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 20:

Comparison of microarrays and qPCR results. This table shows the fold change obtained from both microarrays and qPCR for significantly regulated genes (that were validated by qPCR).

Format: XLS Size: 47KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 21:

miRNA:target inverse relationship. This table shows the predicted miRNA:mRNA inverse relationship for significantly regulated genes and 9 selected miRNAs. The expression of these nine miRNAs was validated by qPCR. Only those miRNA:mRNA pairs are shown that are predicted by atleast two tools and show inverse correlation to each other.

Format: XLS Size: 49KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data