InterJournal Complex Systems, 179
Status: Accepted
Manuscript Number: [179]
Submission Date: 980313
Comment on manuscript revision number 5194
Response to referees for "Genetic Network Inference"
Author(s): Stefanie Fuhrman

Subject(s): CX.3, BG.2, BG.14

Category: Brief Article

Abstract:

We appreciate the critical comments of the reviewers and have revised the manuscript accordingly. In response to the anonymous reviewer (ms #159), we have included a more explicit statement in the second paragraph of the Results regarding our choice of genes, and have added a brief statement to the Discussion (sixth paragraph) about the limitations of using whole tissue homogenate. In response to David Fell (ms # 176), the unclear sentence in the second paragraph of the Methods now reads, “We chose to include slopes as well as expression values . . . “. Sui Huang (ms #165) has pointed out the absence of a gel figure. We have therefore included in the Introduction, Methods, and Results, a reference to our PNAS (1998 Jan. 6) paper, Wen et al., to make available the images of our PCR products; these images demonstrate the uniformity of the triplicate assays. Wen et al. also contains a figure showing that most product/control ratios were close to 1, suggesting that the PCR reactions were unlikely to have gone as far as the plateau range. (Unfortunately we cannot perform calibration reactions for so many genes) We have also improved and shortened the abstract. In addition, we have included a sentence about the novelty of this study at the end of the Introduction. The issue of possible apoptosis-related effects on gene expression measurements is now mentioned in the sixth paragraph of the Discussion. Regarding Boolean nets, we mention them as a point of interest in this paper, but may discuss possible relations between Boolean nets and large-scale temporal gene expression patterns in more detail in future publications. See http://rsb.info.nih.gov/mol-physiol/ICCS/inference/ICCS.html for the revised version described above. We hope the reviewers find these changes satisfactory.

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