• SJSU Singular Matrix Database
  • Matrix group: Pajek
  • Click here for a description of the Pajek group.
  • Click here for a list of all matrices
  • Click here for a list of all matrix groups


  • Matrix: Pajek/yeast
  • Description: Pajek network: yeast protein interaction network
  • download as a MATLAB mat-file, file size: 132 KB. Use SJget(227) or SJget('Pajek/yeast') in MATLAB.
  • download in Matrix Market format, file size: 55 KB.
  • download in Rutherford/Boeing format, file size: 52 KB.

    Pajek/yeast

    Routine svd from Matlab 7.6.0.324 (R2008a) used to calculate the singular values.

    Pajek/yeast

    scc of Pajek/yeast

    Matrix properties (click for a legend)  
    number of rows2,361
    number of columns2,361
    structural full rank?no
    structural rank1,659
    numerical rank 1,644
    dimension of the numerical null space717
    numerical rank / min(size(A))0.69632
    Euclidean norm of A 19.486
    calculated singular value # 16440.016375
    numerical rank defined using a tolerance
    max(size(A))*eps(norm(A)) =
    8.388e-012
    calculated singular value # 16459.7047e-015
    gap in the singular values at the numerical rank:
    singular value # 1644 / singular value # 1645
    1.6873e+012
    calculated condition number9.3684e+066
    condestInf
    nonzeros13,828
    # of blocks from dmperm579
    # strongly connected comp.101
    explicit zero entries0
    nonzero pattern symmetrysymmetric
    numeric value symmetrysymmetric
    typebinary
    structuresymmetric
    Cholesky candidate?yes
    positive definite?no

    authorS. Sun, L. Ling, N. Zhang, G. Li, R. Chen
    editorV. Batagelj
    date2003
    kindundirected graph
    2D/3D problem?no
    SJid227
    UFid1,533

    Additional fieldssize and type
    PIN_classfull 2361-by-1
    nodenamefull 2361-by-154

    Notes:

    ------------------------------------------------------------------------------
    Pajek network converted to sparse adjacency matrix for inclusion in UF sparse 
    matrix collection, Tim Davis.  For Pajek datasets, See V. Batagelj & A. Mrvar,
    http://vlado.fmf.uni-lj.si/pub/networks/data/.                                
    ------------------------------------------------------------------------------
     Yeast protein interaction / long names                                       
     ---------------------------------------                                      
     Dongbo Bu, etal.: Topological structure analysis of the                      
     protein-protein interaction network in budding yeast.                        
     Nucleic Acids Research, 2003, Vol. 31, No. 9 2443-2450                       
     http://www.bioinfo.org.cn/PIN/                                               
     http://www.imb-jena.de/jcb/ppi/PPI_PDF_free/bu2003.pdf                       
                                                                                  
     transformed in Pajek format: V. Batagelj, 25. July 2003                      
     -----                                                                        
     Yeast protein interaction / PIN class                                        
     -------------------------------------                                        
     Dongbo Bu, etal.: Topological structure analysis of the                      
     protein-protein interaction network in budding yeast.                        
     Nucleic Acids Research, 2003, Vol. 31, No. 9 2443-2450                       
     http://www.bioinfo.org.cn/PIN/                                               
                                                                                  
     transformed in Pajek format: V. Batagelj, 25. July 2003                      
     PIN class encoding:                                                          
     1-T, 2-M, 3-U, 4-C, 5-F, 6-P, 7-G, 8-D, 9-O, 10-E, 11-R, 12-B, 13-A          
     -----                                                                        
    

    Ordering statistics:AMD METIS
    nnz(chol(P*(A+A'+s*I)*P'))56,350 65,872
    Cholesky flop count8.6e+006 1.0e+007
    nnz(L+U), no partial pivoting110,339 129,383
    nnz(V) for QR, upper bound nnz(L) for LU477,562 379,602
    nnz(R) for QR, upper bound nnz(U) for LU435,401 509,794

    Maintained by Leslie Foster, last updated 24-Apr-2009.

    Entries 5 through 14 in the table of matrix properties and the singular
    value plot were created using SJsingular code. The other plots
    and statistics are produced using utilities from the SuiteSparse package.
    Matrix color plot pictures by cspy, a MATLAB function in the CSparse package.