Signification of data files (in folders WORK_XX) --------------------------------------------------------------------- 1) G-matrix files for different variants of reduced Google matrix with extension G*.txt (i) Name format: GXX_NETWORK_GROUPNAME_dalpha_Nr.YYY.txt with XX=pr, qr, R, rr, rrplusGqr rrSIGNGqr for 6 G-matrix variants (see below in (iii) for explanations). NETWORK = name of used basis network, e.g. here: SIGNOR PPI network of April 2017 GROUPNAME = name of group of nodes used, e.g. here "WORK_EJ" (for injection/absorption at "EGFR P00533 (+)/ JAK2 O60674 (-) (")) dalpha=1-alpha (=1-0.85=0.15) with alpha beeing the ususal damping factor Nr = matrix dimension, e.g. here: 40 YYY=one of five possibilities total_order, rwo_wise column_wise, friends, followers corresponding to different ordering of matrix elements (see below in (ii) for more details) (ii) Content format: There are 6 columns with each line representing one matrix element G(i,j) The columns are: i, j, value of G(i,j), name of node i, the symbols "###" (to better separate visually both node names) and finally name of node j all separated by tab-symbols ("\t" in C). Note that now everywhere node numbers (either groups or total network) start with 1 (and no longer with 0). ordering variants: total_order: The lines are ordred with decreasing values of G_{ij} for ALL elements i,j. row_wise (or *.dat instead of "*row_wise.txt"): The index j is moving faster with line number of file. The blocks corresponding to one value of i ("one matrix row") are separated by an empty line. column_wise: The index i is moving faster with line number of file. The blocks corresponding to one value of j ("one matrix column") are separated by an empty line. followers: The index j is ordered with decreasing values of G_{ij} inside each block of i for one matrix row giving the followers of node i. friends: The index i is ordered with decreasing values of G_{ij} inside each block of j for one matrix column giving the friends of node j. (iii) Signification of different G-matrix variants: The names GR etc. correspond (mostly) to the definitions of the paper: Eur. Phys. J. B (2016) 89: 269 in detail: Grr is defined as the 11-Block of eq. (3) of the above paper and corresponds to the direct links inside the group of nodes. GR is the full reduced Google matrix given by eqs. (8) and (16). Gpr is the main projector part given by eq. (17). Gqr is the given by eq. (18). (GI = Gpr + Gqr is the full "indirect" or Interaction contribution, also given by the second term of second equation in (8), no longer given here since it is less important) GrrSIGNGqr is the sum of Grr and Gqr but only using non-diagonal terms of Gqr (the large diagonal elements of Gqr are not taken into account here). Here the sign is kept and no renormalization of columns is done. G*plus2minus => gives transitions from block of positive P_1 values to block of negative P_1 values (ordered by G-matrix element value, largest values on top) G*minus2plus => gives transitions from block of negative P_1 values to block of positive P_1 values (ordered by G-matrix element value, largest values on top) (iv) the File Gweight_(....).dat gives the realive weights of the these G-matrices. Note that GrrplusGqr (=RA(Grr+Gqr) has allways weight 1 due to the renormalization which is purely artifical. 2) Gmatrix files with extensions G*.mat/G*.png: (i) Name format: GXX_NETWORK_GROUPNAME_Nr.mat/.png similar as above. (ii) Content format of G.mat: 1st line: => Nr^2 2nd line: => Nr further lines all matrix elements G(i,j) with i=1,...,Nr outer loop and j=1,...,Nr inner loop (i.e. Nr lines in file for first row of G, than Nr lines for second row etc.). These files are more suitable for input in other programs (e.g. creation of density plots etc.). (iii) G*.png: raw density plot png files obtained from G.mat files 3) pagerank files: (i) Name fomat: pagerank_YYYY_GROUPNAME_NETWORK_ALPHA.dat with GROUPNAME and NETWORK as above, ALPHA=0.15 = 1-damping factor with damping factor = 0.85). YYYY corresponds to: "full" => full PageRank vector of the NETWORK "left" => left eigenvector of G_{ss} (see page 4, first column, last paragraph of above paper for explanations). "right" => right eigenvector of G_{ss}; note that the latter two were crucial to compute GR etc. according to eqs. (12) to (18). "small" => the PageRank vector of the reduced Google matrix GR "GrrplusGqr" => the PageRank vector of the effective Google matrix GrrplusGqr as explained above, the latter two were directly computed by the powermethod using the small reduced matrices Now here all node indices and Kranks etc. are starting with 1 (and no longer 0) These files are ordered in decreasing PageRank values and contain also node names (ii) Content format: first line: "# size = further lines: four columns and the lines are ordered according to K-index of each vector (i.e. first line => largest value of vector etc.). 1st column = K-index (note in the file K-index starts with 1 and no longer 0), 2nd column = the value of the vector 3rd column = original node index (also starting with 1) 4th column = node name 4) subpagerank files (i) Name format: similar as above but name starting with "subpagerank" instead of "pagerank" (ii) Content format: These file give the different (pagerank and other) vectors but only in the small space of reduced nodes with 6 columns which ares explained in second lines of each each file: # reduced index, value, normalized value, original index, K index, name For the three cases full, left and right the normalization changes from big to small network. For left and right the shown vectors are not \psi_L/R (which are actually "0" on reduced nodes !) but the related vectors in small space given by a=G_{rs}\psi_R and b=G_{sr}^T\psi_L such that G_{pr}=ab^T according to eq. (17) of above paper. Here G_{rs} and G_{sr} are the 12 and 21 blocks in (3). For small and GrrplusGqr "small" and "big" space are the same (i.e. only "small" space). These files are NOT PageRank ordered but there are in original Group-node order. 5) Data files for subgroup selection of type ZZ* with ZZ=EJ (for "EGFR/JAK2") which are: ZZ.txt: ascii file with the two nodes names for injection/absorption ZZ_pm_40.all: file of subgroup of 20 top negative P_1 and 20 top positive P_1 with 6 columns: Rank of |P_1|, Krank, PageRank value, P_1 value, original index in network, protein name in network 6) PageRank magnetization values are given "mag_PPI.dat" for all SIGNOR proteins; for each group (EJ, ME, EP) magnetization is given in "maggroup_PPI_ME_39.dat" (ME is group name); image of group magnetization on local PageRank-CheiRank plane (K,K*) is given in maggroup_PPI_ME_39.png