Supplementary Materials

Supplementary Materials for:

Genome-Wide Analysis of a Wnt1-Regulated Transcriptional Network Implicates Neurodegenerative Pathways

Eric M. Wexler,* Ezra Rosen, Daning Lu, Gregory E. Osborn, Elizabeth Martin, Helen Raybould, Daniel H. Geschwind

*To whom correspondence should be addressed. E-mail: ewexler{at}

This PDF file includes:

  • Methods
  • References
  • Fig. S1. Wnt1 differentially modulates Wnt pathway genes across time.
  • Fig. S2. Wnt1 induces significant early enrichment of genes involved in survival signaling, energy metabolism, and biosynthesis (anabolism).
  • Fig. S3. Wnt1 induces significant later enrichment of genes involved in blood vessel development, axonogenesis, and Huntington's disease.
  • Fig. S4. Dynamic time warping (DTW) sensitivity analysis of simulated expression data.
  • Fig. S5. DTW sensitivity analysis of experimental data.
  • Fig. S6. DTW identifies Wnt1 effects on cancer-related genes.
  • Fig. S7. Demonstration of robust blind source separation using parallel independent component analysis (pICA).
  • Fig. S8. Overview of mutual information–based network inference and sensitivity to thresholding effects.
  • Fig. S9. Scalable version of Fig. 2: Wnt1 modulates genes implicated in Wnt signaling and Alzheimer's disease (AD).
  • Fig. S10. Scalable version of Fig. 3: Unsupervised pICA blindly separates gene expression patterns by biological function.
  • Fig. S11. Scalable version of Fig. 4: Combined topological overlap–based clustering and dynamic Bayesian network construction links Wnt1 signaling with changes in dementia-related genes.
  • Fig. S12. Scalable version of Fig. 5: Wnt1 induces a gene expression architecture that correlates many well-known dementia genes with Wnt-related signal transduction.

[Download PDF]

Technical Details

Format: Adobe Acrobat PDF

Size: 7.11 MB

Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Overlap of gene changes across time.
  • Table S2 (Microsoft Excel format). Wnt1-induced immediate changes in known Wnt-related genes.
  • Table S3 (Microsoft Excel format). Wnt1-mediated enrichment of GO and KEGG pathways varies across epochs.
  • Table S4 (Microsoft Excel format). Wnt-1 induces changes in genes implicated in AD by genetic association studies.
  • Table S5 (Microsoft Excel format). GO analysis of whole time series DTW-identified genes.
  • Table S6 (Microsoft Excel format). Extended ICA gene list and ontology analysis table.
  • Table S7 (Microsoft Excel format). ICA-GO sensitivity analysis.
  • Table S8 (Microsoft Excel format). Gene Set Enrichment Analysis of ICA module genes probed against the Broad Institute's Molecular Signatures Database (MSigDB).
  • Table S9 (Microsoft Excel format). Unique, independent statistical analyses identify similar Wnt1-mediated changes in gene expression.

[Download Tables S1 to S9 (Compressed)]

Technical Details

Format: Microsoft Excel. Files are packaged as a compressed archive, in *.zip format; users should download the compressed file to their machine and decompress the file on their local hard drive, using the instructions below.

Size: 2.08 MB (compressed); 5.05 MB (decompressed)

Instructions for downloading and decompressing files:

  1. Create a temporary folder on your machine's hard drive.
  2. Save the compressed archive to the temporary folder you created, using the links above.
  3. Decompress the compressed file in the temporary folder using decompression software such as WinZip (Windows; or StuffIt Expander (Windows and Mac;

Citation: E. M. Wexler, E. Rosen, D. Lu, G. E. Osborn, E. Martin, H. Raybould, D. H. Geschwind, Genome-Wide Analysis of a Wnt1-Regulated Transcriptional Network Implicates Neurodegenerative Pathways. Sci. Signal. 4, ra65 (2011).

© 2011 American Association for the Advancement of Science