Supplementary information

From the following article:

Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis Kristin C. Gunsalus, Hui Ge, Aaron J. Schetter, Debra S. Goldberg, Jing-Dong J. Han, Tong Hao, Gabriel F. Berriz, Nicolas Bertin, Jerry Huang, Ling-Shiang Chuang, Ning Li, Ramamurthy Mani, Anthony A. Hyman, Birte Sönnichsen, Christophe J. Echeverri, Frederick P. Roth, Marc Vidal and Fabio Piano Nature 436, 861-865 (11 August 2005)

Supplementary Methods

This file contains a description of the methods used in the main text. Supplementary Methods - Download Word file (149KB)

Supplementary Figure S1a

Phenoclustering of 661 genes required for early embryogenesis. A global view with numbered clusters and enriched GO annotations labelled, and highlighting clusters containing proteins tested by localization. Supplementary Figure S1a - Download PDF file (2.6MB)

Supplementary Figure S1b

An expanded view showing all gene names. Supplementary Figure S1b - Download PDF file (5.5MB)

Supplementary Figure S2

Global correlations between interactome, transcriptome, and phenome data for the EE dataset, excluding ribosomal and proteasomal genes. Supplementary Figure S2 - Download PDF file (772KB)

Supplementary Figure Legends

Legends for Supplementary Figures S1 and S2. Supplementary Figure Legends - Download Word file (25KB)

Supplementary Table S1

Fly-to-worm interologues for high-confidence D. melanogaster Y2H interactions from Giot et al., 2003. Joint e-values and percent identities over the lengths of the query and target proteins are indicated. See Supplementary Methods for details. Supplementary Table S1 - Download Excel file (154KB)

Supplementary Table S2

Functional characteristics (Gene Ontology (GO) terms) enriched in phenoclusters from Fig. 1b and Supplementary Fig. S1. Supplementary Table S2 - Download Excel file (30KB)

Supplementary Table S3

Comparison of EE 'within-set' network versus random within-set networks from WI7 (see Supplementary Methods for selection of random gene sets from WI7). Supplementary Table S3 - Download Excel file (37KB)

Supplementary Table S4

Analysis of shared GO functional annotations within EE networks. Supplementary Table S4 - Download Word file (45KB)

Supplementary Table S5

Analysis of shared GO functional annotations within EE networks, considering only gene pairs for which both members have some GO annotation. Supplementary Table S5 - Download Word file (25KB)

Supplementary Table S6

Modular organization of the multiple support network. a, Summary of molecular machine models. b, Triple support network. c, Multiple support network. (d.q) Individual molecular models from the multiple support network: d, Ribosome; e, Proteasome; f, F1F0 ATPase; g, Vacuolar ATPase; h, Anaphase promoting complex (APC); i, Polarity; j, Actins; k, Microtubule (MT) cytoskeleton; l, Histones; m, Chromosome maintenance and nuclear membrane function; n, mRNA and protein metabolism; o, Translation initiation; p, COPI coatomer complex; q, Oocyte integrity and meiosis. Supplementary Table S6 - Download Excel file (1MB)

Supplementary Data File S1

These two files contain the set of gene/protein interactions describing the entire integrated network for 661 EE genes based on a compendium of interactome, transcriptome, and phenome data, as presented in Figure 3a. As in the figure, links between genes/proteins with multiple degrees of support have been merged into single edges for visual clarity. These data are provided in Cytoscape format (http://www.cytoscape.org). This file is a Cytoscape simple interaction file (SIF) containing pairwise interactions. .pp., protein interaction; .pc., phenocorrelation; .ec., expression correlation. Multiple support edges are indicated by combinations of these three abbreviations (.pppc., .pcec., .ppec., and .pppcec.). Supplementary Data File S1 - Download SIF file (618KB)

Supplementary Data File 2

Cytoscape node attribute (NOA) file translating cosmid names to 3-letter gene names. Supplementary Data File 2 - Download NOA file (10KB)

Supplementary Movie S1

These ten movie files are time-lapse movies of all localization studies of expressed protein-GFP fusions in the early C. elegans embryo. This movie shows GFP.T26A5.8 localization in C. elegans during early embryogenesis. The localization is intensely nuclear at interphase and weakly chromosomal at metaphase, with some cytoplasmic punta. Time stamp, in minutes, is shown. Supplementary Movie S1 - Download Movie (4MB)

Supplementary Movie S2

This movie shows GFP.F35B12.5 localization in C. elegans during early embryogenesis. The localization appears centriolar and transiently on the spindle. Time stamp, in minutes, is shown. Supplementary Movie S2 - Download Movie (882KB)

Supplementary Movie S3

This movie shows GFP.Y45F10D.9 localization in C. elegans during early embryogenesis. The localization appears centriolar and transiently on the spindle. Time stamp, in minutes, is shown. Supplementary Movie S3 - Download Movie (4.1MB)

Supplementary Movie S4

This movie shows GFP.W08F4.8 localization in C. elegans during early embryogenesis. There is a nuclear .flash. at mitosis and nuclear exclusion at interphase. Time stamp, in minutes, is shown. Supplementary Movie S4 - Download Movie (3.4MB)

Supplementary Movie S5

This movie shows GFP.C38D4.3 localization in C. elegans during early embryogenesis. The signal is diffused in the nucleus and enriched on the nuclear periphery at telophase to the next mitosis, when chromosomes form and are labelled in a way that eventually resemble kinetochore enrichment. Time stamp, in minutes, is shown. Supplementary Movie S5 - Download Movie (5.5MB)

Supplementary Movie S6

This movie shows GFP.T24F1.2 localization in C. elegans during early embryogenesis. Nuclear envelope enrichment. Time stamp, in minutes, is shown. Supplementary Movie S6 - Download Movie (2.7MB)

Supplementary Movie S7

This movie shows GFP.C29E4.2 localization in C. elegans during early embryogenesis. Condensing chromosomes are labeled. Time stamp, in minutes, is shown. Supplementary Movie S7 - Download Movie (1MB)

Supplementary Movie S8

This movie shows GFP.Y55B1BR.3 localization in C. elegans during early embryogenesis. Diffused nuclear localization during interphase and not visible in nucleus at mitosis. Time stamp, in minutes, is shown. Supplementary Movie S8 - Download Movie (9.2MB)

Supplementary Movie S9

This movie shows GFP.F55C5.4 localization in C. elegans during early embryogenesis. Localization on condensing chromosomes is visible with a typical kinetochore pattern. Time stamp, in minutes, is shown. Supplementary Movie S9 - Download Movie (5.3MB)

Supplementary Movie S10

This movie shows GFP.T10B5.6 localization in C. elegans during early embryogenesis. Localization on condensing chromosomes is visible with a typical kinetochore pattern. Time stamp, in minutes, is shown. Supplementary Movie S10 - Download Movie (2.6MB)