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Sci. Signal., 26 February 2013
[DOI: 10.1126/scisignal.2003266]

Supplementary Materials for:

A Systems Approach for Decoding Mitochondrial Retrograde Signaling Pathways

Sehyun Chae, Byung Yong Ahn, Kyunghee Byun, Young Min Cho, Myeong-Hee Yu, Bonghee Lee,* Daehee Hwang,* Kyong Soo Park*

*To whom correspondence should be addressed. E-mail: dhhwang{at}postech.ac.kr (D.H.); kspark{at}snu.ac.kr (K.S.P.); bhlee{at}gachon.ac.kr (B.L.)

This PDF file includes:

  • Fig. S1. Association of DEGs with cellular processes and genes that have been previously reported to be affected by the mt3243 mutation.
  • Fig. S2. Differential expression of TFs known to participate in mitochondrial retrograde signaling.
  • Fig. S3. Knockdown of RXRA using siRNA.
  • Fig. S4. Regulation of mRNA and protein abundances of RXRA through JNK activated by ROS.
  • Table S1. Mitochondria-to-nucleus retrograde signaling mediators, signaling pathways, and their downstream TFs.
  • Table S2. Organizing the 2404 DEGs into clusters and their differential expression patterns among the three types of cells.
  • Table S5. TF-target interactions collected from the six databases.
  • Table S11. Primary antibodies used for Western blotting analysis and immunofluorescence analysis.
  • Table S12. Primer sequences used in qRT-PCR analysis.
  • Tables S3, S4, S6 to S10 legends

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Other Supplementary Material for this manuscript includes the following:

  • Table S3 (Microsoft Excel format). The lists of the genes included in the individual clusters.
  • Table S4 (Microsoft Excel format). GO Biological Processes enriched in the DEGs in the individual clusters.
  • Table S6 (Microsoft Excel format). Seventy-two TFs that could potentially be involved in retrograde signaling induced by the mt3243 mutation.
  • Table S7 (Microsoft Excel format). The OXPHOS genes differentially expressed in cells containing the mt3243 mutation.
  • Table S8 (Microsoft Excel format). One hundred sixty-three DEGs that showed an increase in mRNA abundances in 3243G M cells by the RA treatment.
  • Table S9 (Microsoft Excel format). The translation-related genes differentially expressed in cells containing the mt3243 mutation.
  • Table S10 (Microsoft Excel format). One hundred eighty TFs that showed altered mRNA abundance in cells containing the mt3243 mutation.

[Download Tables S3, S4, S6-S10]

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Citation: S. Chae, B. Y. Ahn, K. Byun, Y. M. Cho, M.-H. Yu, B. Lee, D. Hwang, K. S. Park, A Systems Approach for Decoding Mitochondrial Retrograde Signaling Pathways. Sci. Signal. 6, rs4 (2013).

© 2013 American Association for the Advancement of Science

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