Files in Supplementary Information to Rual et al, Nature 2005. "Towards a proteome-scale map of the human protein-protein interaction network".

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PLEASE NOTE: IF YOU ARE LOOKING FOR YEAST 2-HYBRID INTERACTION DATA GENERATED TOWARDS THIS PAPER 
(i.e., THE "CENTER FOR CANCER SYSTEMS BIOLOGY-HUMAN INTERACTOME VERSION1" , OR "CCSB-HI1" DATA SET), 
THEY ARE AVAILABLE IN SUPPLEMENTARY TABLE 2 IN THE FILE ENTITLED "SupTable2.xls". 
HERE, EVERY LINE WITH A '+' IN THE 'Y2H' COLUMN REFERS TO A Y2H INTERACTION THAT IS PART OF THE CCSB-HI1 DATA SET.
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1) Rual_etal_Nature2005.pdf : PDf version of the main paper.

2) Rual_etal_Supplement.doc: MS-WORD file contains expanded information regarding various concepts discussed in the Rual et al main paper, plus a Methods section. The file has the following sections:

I. Definition of the human interactome
II. Interactome maps as scaffold information
III. Iterative approach to the human interactome mapping project
IV. High-specificity Y2H
V. Systematic high-throughput Y2H system
VI. Removing lower confidence Y2H interactions
VII. Public release of CCSB-HI1
VIII. Estimating specificity
IX. Technical False Positives
X. Increasing coverage of Y2H data sets
XI. Correlations between CCSB-HI1 and other biological information
XII. Interpretation of overlap with other biological attributes
XIII. Global properties of the CCSB-HI1 network
XIV. Models of novel molecular modules
XV. CCSB-HI1 and human disease

In addition, the file has a Methods section and legends for Supplementary Figures and Tables.


3) Sup.Fig.1.pdf : Filtering and quality assessment of Y2H interactions. Format: PDF file.

4) Sup.Fig.2.pdf : Bias in network neighborhoods for either CCSB-HI1 or LCI interactions. Format: PDF file.

5) Sup.Fig.3.pdf : Occurrence of CCSB-HI1-associated, LCI-associated associated gene pairs in Pubmed or Google Scholar searches. Format: PDF file.

6) Sup.Fig.4.pdf : Correlation of interaction data with other gene- or protein-pair characteristics. Format: PDF file.

7) Sup.Fig.5.pdf : Network analyses of CCSB-HI1. Format: PDF file

8) Sup.Fig.6.pdf : Sub-networks of putative biological modules. Format: PDF file.

9) SupTable1.xls : List of all human ORFs in Space-I that were tested for Y2H interactions. Format: Tab-separated text file.

Description of fields:
hORFeome ID - hORFdb (http://horfdb.dfci.harvard.edu/)  ID
Entrez gene ID - Entrez Gene (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) ID
GeneBank accession - GenBank accession for the ORF 	
MGC - Genbank accession of the MGC cDNA clone from which the ORF was derived

10) SupTable2.xls : List of CCSB-HI1 and LCI binary interactions along with annotation of whether they were tested in co-AP assays and whether they showed correlation with other biological attributes. 
Interactions are listed are A-B pairs where EntrezGeneIDA is always <= EntrezGeneIDB. Note that interactions are non-directional, i.e., A-B and B-A are equivalent. Format: Tab-separated text file.

Description of fields:   
Y2H - a '+' in this column refers to a Y2H interaction in the CCSB-HI1 data set.

LCI - an entry of 'core', non_core' or 'hyper_core' in this column refers to an interaction in that corresponding subset of the Literature-Curated data set in Space-I (LCI).  

co-AP result - an entry of '+', '-', or 'NA' in this column refers to an interaction that was re-tested in the GST pull-down co-affinity purification assay.
'+' refers to an interactions that was scored as positive in the co-AP,'-' refers to an interaction that was negative in the co-AP and 'NA' refers to cases where the co-AP assay was uninterpretable (see "Methods" for details).   

co-AP lane - Gives lane position of pairs tested in the co-AP as shown in Fig 1b and Fig S1b.

Co-expression Su - a '+' in this column refers to a Y2H or LCI interacting protein pair whose mRNAs were co-expressed in the Su et al data set.

Co-expression Zhang - a '+' in this column refers to a Y2H or LCI interacting protein pair whose mRNAs were co-expressed in the Zhang et al data set.    

Co-exprssion Johnson - a '+' in this column refers to a Y2H or LCI interacting protein pair whose mRNAs were co-expressed in the Johnson et al data set.

Co-expression Shyamsundar - a '+' in this column refers to a Y2H or LCI interacting protein pair whose mRNAs were co-expressed in the Shyamsundar et al data set.

Share Mouse Phenotype - a '+' in this column refers to a Y2H or LCI interacting protein pair which have mouse orthologs sharing a common specific mouse phenotype.

Share upstream motif - a '+' in this column refers to a Y2H or LCI interacting protein pair whose genes share a common specific upstream motif.

Share GO process - a '+' in this column refers to a Y2H or LCI interacting protein pair that share a common specific Gene Ontology "Process" term.

Share GO function - a '+' in this column refers to a pair of Y2H or LCI interacting protein pair that share a common specific Gene Ontology "function" term.

Share GO component - a '+' in this column refers to a Y2H or LCI interacting protein pair that share a common specific Gene Ontology "component" term.


11) SupTable3.xls : List of CCSB-HI1 and LCI interactions that were tested in co-AP experiments. Format: Tab-separated text file.

12) SupTable4.xls : List of over-represented and under-represented Pfam-A domains in CCSB-HI1 and LCI data sets. Format: MS-EXCEL file.

13) SupTable5.xls : Analysis of overlap between CCSB-HI1 or LCI-interacting protein-pairs with other shared gene- or protein-pair characteristics. Format: Tab-separated text file. See Table legend in Supplementary information file for detailed description of fields.

14) SupTable6.xls : Statistics of CCSB-HI1 interactions between proteins in different evolutionary classes. Format: MS-EXCEL file.

15) SupTable7.xls : List of 172 MCODE-generated clusters from the CCSB-HI1 network and the combined CCSB-HI1/LCI and CCSB-HI1/LC networks. Format: Tab-separated text file.

16) SupTable8.xls : Potentially novel associations of proteins with genetic disorders as revealed by the CCSB-HI1 interaction data set. Format: MS-EXCEL file.

17) SpaceI-ORF-sequences.tsv : Entrez Gene IDs, Genbank accessions and DNA sequences corresponding to the ORFs tested for interactions in Space-I.

18) HI_psi_mi.xml: List of CCSB-HI1 interactions in PSI-MI format (Hermjakob H et al, Nat Biotech. 2004)

19) HI_biopax.owl: List of CCSB-HI1 interactions converted from PSI-MI to BioPAX format