LUMC: LOPAC screen analysis

Transcription

1 LUMC: LOPAC screen analysis Preliminary results November 9, 2012 This document briefly presents the results from the LOPAC compounds screen performed at LUMC. It contains the following information: The set of all protein targets that were targeted by at least one compound - AllProteinTargets uniprot.csv (Section 1) List of compounds and the proteins that they target - Lopac2Target uniprot.csv and Lopac2Target bin uniprot.csv (Section 1) Pruned list of protein targets. For both Mtb and Stm - LopacFiltered joint.csv. For Mtb - LopacFiltered Mtb.csv. For Stm - LopacFiltered Stm.csv (Section 2) Gene to gene interactions (provided in a separate file) - g2g.txt. Gene annotations with terms from Gene Ontology (provided in a separate file) - g2ont.txt. Results from predictive clustering trees. Results from feature ranking. Results from predictive clustering trees including the info about cell viability. 1 Protein targets We describe each compound from the LOPAC library with the protein targets for which was showed the given compound is active. From the 1260 compounds in the library, 967 compounds were found to be active on human protein targets. In the further analysis, we include only those. Furthermore, we identified 760 (human) protein targets for which at least one LOPAC compound was found active. The proteins are given by their Uniprot ID. The list of protein targets is given in a separate file (AllProteinTargets uniprot.csv). The association of each LOPAC compound to the targets is given first in the file Lopac2Target.csv, where each row represents a compound. Each compound is identifeid by its LOPAC catnum (the first field in the row), and then the protein targets (i.e., the respective accession number ids) are listed. Furthermore, we provide a matrix with dimensions in file Lopac2Target bin.csv. Here, each row presents a compound and each column is a protein target. Note that, the first row contains the protein accession numbers, while the first column contains the LOPAC catnum identifeirs. 1

2 2 Prunning of the protein targets The number of 760 target proteins is large and it includes protein that are targeted by a large variety of compounds. Typically, these proteins are not specific and closely relevant for the Mtb and Stm measurements. Furthermore, more interesting are the protein targets that were found active in studies involving hit compounds (compounds with z-score larger than 2 or smaller than -2) and not active in the remainder of the compounds. To this end, we prune the set of the proteins using the following rule: A protein target is removed from the set of protein targets if at least 90% of the compounds that are targeted by are not identified as hits. Considering this, we provide three separate lists of compounds and the respective protein targets. The first list (given in the file LopacFiltered joint.csv) gives the protein targets that are obtained when the hit compounds were defined using both Mtb and Stm z-score values. The second list (given in the file LopacFiltered Mtb.csv) gives the protein targets that are relevent for the hit compounds for the Mtb study. The third list (given in the file LopacFiltered Stm.csv) gives the protein targets relevant for the hit compounds for the Stm study. We further briefly show the gene networks obtained from the pruned protein targets using STRING. First, we give the network for both Mtb and Stm (the 44 proteins given in the file LopacFiltered joint.csv). Then, we show the network for Mtb (the 41 proteins from file LopacFiltered Mtb.csv). Finally, we present the network for Stm (the 11 proteins from file LopacFiltered Stm.csv) 3 Interactions and annotations We describe each of the targets with the Gene Ontology (GO) and KEGG terms that are annotated with. Afterwards, for each compound, we take the union of the GO terms from each protein target that the given protein was described with. The file that contains the GO and KEGG annotations is g2ont.txt. Next, we include the interactions of the annotated proteins. Namely, using the file g2g.txt, each compound is described with the union of the GO and KEGG terms for each of the proteins and additionally, the union of the GO and KEGG terms that the interacting proteins are annotated with. 4 Resuls from Feature Ranking Here, we present the results obtained by ReliefF feature ranking algorithm (from WEKA toolbox). Instead of given the complete list, we present the proteins networks for Mtb and Stm for both numeric and discrete values of the z-score. 2

3 Figure 1: The protein network for both Mtb and Stm. 3

4 Figure 2: The protein network for Mtb. Figure 3: The protein network for Stm. 4

5 Figure 4: The protein network for the top 50 proteins for Mtb numeric. 5

6 Figure 5: The protein network for the top 50 proteins for Mtb discrete. 6

7 Figure 6: The protein network for the top 50 proteins for Stm numeric. 7

8 Figure 7: The protein network for the top 50 proteins for Stm discrete. 8

9 5 Results from PCTs with cell viability info This section includes the results from the analysis of the data using predictive clustering trees (PCTs). We present the results in three sub-sections, each dealing with the specific representation of the protein targets and therefore the compounds. In other words, the three scenarios differ in the descriptive attributes, while the target attributes are always the same: the z-scores for each compound. For each of the scenarios we present the result for the real values of the z-scores and the discretized counterparts (positive and negative hit ). The results shown here, besides the bacterial load, also have the z-score for cell viability as target variables. The first value in the tree leafs is for bacterial load and the second value is for cell viability. In this scenario, we are more focused on two outcomes of the application of the compounds: kill bacteria - do nothing to host and promote bacteria - do nothing to host. We are however not interested in the outcomes where nothing happens to the bacteria or both bacteria and the host are killed. Interesting outcomes are also: kill bacteria - promote host and promote bacteria - promote host. However, in this analysis we do not consider them since they do not appear in any of the PCTs, probably because there is no specific GO term or protein target that offers a good differentiation between these conditions and the rest of the conditions. In the respective section, we give a short overview of each PCT in the context of the three outcomes of compounds application. 5.1 Uniprot protein identifiers Mtb - numeric A2TJX0 +--yes: [-0.12, ]: 4 compound: [C9911,C9754,P4405,O3125] +--no: F1D8R8 +--yes: [-0.866, ]: no: Q9BYT3 +--yes: [-1.47, ]: no: P yes: [0.435,-7.01]: 2 compound: [C6645,M6383] +--no: P yes: [-5.305,-1.23]: 2 compound: [S8442,S9692] +--no: [ , ]: 912 compound: [...] A2TJX0: Krueppel-like factor 5 F1D8R8: Steroidogenic factor 1 nuclear receptor Q9BYT3: Serine/threonine-protein kinase P05067: Amyloid beta A4 protein P07949: Proto-oncogene tyrosine-protein kinase recept In this tree, most interesting is the group of compounds that consists of S8442 and S9692, which when applied kill the bacteria and do nothing to the host. Namely, this happens when the protein P07949 is targeted. 9

10 5.1.2 Mtb - discrete F1D8R8 +--yes: [0,-1] [9.0,10.0]: no: A2TJX0 +--yes: [1,-1] [2.0,3.0]: 3 compound: [C9911,C9754,O3125] +--no: Q9BYT3 +--yes: [0,0] [24.0,23.0]: no: P yes: [-1,-1] [1.0,2.0]: 2 compound: [C6645,M6383] +--no: P yes: [-1,-1] [2.0,1.0]: 2 compound: [S8442,S9692] +--no: P yes: [0,0] [36.0,35.0]: no: Q96DE8 +--yes: [-1,0] [2.0,2.0]: 3 compound: [T4318,B8433,C3930] +--no: [0,0] [797.0,839.0]: 865 compound: [...] F1D8R8: Steroidogenic factor 1 nuclear receptor A2TJX0: Krueppel-like factor 5 Q9BYT3: Serine/threonine-protein kinase 33 P05067: Amyloid beta A4 protein P07949: Proto-oncogene tyrosine-protein kinase receptor P43116: Prostaglandin E2 receptor EP2 subtype Q96DE8: PSMD14 protein In this tree, a group of compounds kill the bacteria and do nothing to the host. Thia group consists of the following compounds T4318, B8433 and C3930 and it targets the Q96DE8 protein. 10

11 5.1.3 Stm - numeric Q yes: [10.795,-6.075]: 2 compound: [C9754,M1404] +--no: Q yes: [6.625,-4.105]: 4 compound: [I3766,V1377,P4405,V8879] +--no: O yes: [3.71,-5.18]: 2 compound: [C9911,E1383] +--no: A0PJU7 +--yes: [2.754,-2.488]: 5 compound: [N3510,E1779,N1786,T182,C7522] +--no: P yes: [2.53,-1.916]: 5 compound: [C6645,R5010,T1132,O3125,M6383] +--no: Q yes: [2.46,-2.45]: 2 compound: [A2385,A9809] +--no: [ , ]: 947 compound: [...] Q92793: CREB-binding protein Q04206: Transcription factor p65 O14757: Serine/threonine-protein kinase Chk1 A0PJU7: TSHR protein P05067: Amyloid beta A4 protein Q15788: Nuclear receptor coactivator 1 This tree presents several outcomes where the bacterial load is increased and cell viability is decreased Stm - discrete A2TJX0 +--yes: [1,-1] [3.0,3.0]: 4 compound: [C9911,C9754,P4405,O3125] +--no: F1D8R8 +--yes: [0,0] [10.0,10.0]: no: P yes: O yes: [1,-1] [2.0,2.0]: 2 compound: [C6645,M6383] +--no: [0,0] [2.0,2.0]: 2 compound: [R5010,T1132] +--no: A0PJU7 +--yes: [0,-1] [2.0,2.0]: 3 compound: [N3510,E1779,C7522] +--no: P

12 +--yes: [0,0] [1.0,1.0]: 2 compound: [G0668,C8221] +--no: P yes: [0,-1] [1.0,1.0]: 2 compound: [P108,C5134] +--no: Q9BYT3 +--yes: [0,0] [25.0,24.0]: no: O yes: [-1,0] [1.0,2.0]: 2 compound: [H89,S5567] +--no: P yes: [-1,0] [1.0,2.0]: 2 compound: [P8386,O8757] +--no: Q yes: [0,0] [1.0,2.0]: 2 compound: [N2255,D9766] +--no: F1D8R9 +--yes: [0,0] [2.0,1.0]: 2 compound: [O2139,D8399] +--no: P yes: [0,0] [2.0,1.0]: 2 compound: [A8723,I8250] +--no: Q yes: [0,-1] [2.0,1.0]: 2 compound: [L2167,G6793] +--no: [0,0] [884.0,882.0]: 897 compound: [...] A2TJX0: Krueppel-like factor 5 F1D8R8: Steroidogenic factor 1 nuclear receptor P05067: Amyloid beta A4 protein O60674: Tyrosine-protein kinase JAK2 A0PJU7: TSHR protein P04626: Receptor tyrosine-protein kinase erbb-2 P47901: Vasopressin V1b receptor Q9BYT3: Serine/threonine-protein kinase 33 O75582: Ribosomal protein S6 kinase alpha-5 P02768: Serum albumin Q99808: Equilibrative nucleoside transporter 1 F1D8R9: Liver nuclear receptor homolog-1 variant 2 P21462: fmet-leu-phe receptor Q03181: Peroxisome proliferator-activated receptor In this tree, the most interesting outcome is produced when the protein is targeted by the H89 or S5567. Similarly, when P02768 is targeted the bacterial load is decreased and no harm to the cell viability: P8386 and O8757 target this protein. Furthermore, this tree reveals a connection between the proteins P05067 and O Namely, when both of the proteins are targeted then the bacteria are promoted while the cell viability is reduced. However, if only P05067 is targeted and O60674 is not targets then nothing happens to the bacteria and the host. 12

13 5.2 GO and KEGG terms Mtb - numeric GO yes: [-0.12, ]: 4 compound: [C9911,C9754,P4405,O3125] +--no: GO yes: GO yes: [-4.02, ]: 3 compound: [V1377,V8879,N1786] +--no: [ , ]: no: GO yes: [ , ]: no: GO yes: [-4.33, ]: 3 compound: [A0966,Q3251,S9692] +--no: GO yes: GO yes: GO yes: [-0.995,-0.775]: no: [2.33,-3.4]: 2 compound: [B168,A8598] +--no: GO yes: GO yes: GO yes: [ ,0.75]: 3 compound: [L2167,G6793,F8175] +--no: [ , ]: no: [ , ]: no: GO yes: [-1.235,-3.01]: 2 compound: [A5006,N5751] +--no: [ , ]: no: [1.2525, ]: 4 compound: [T7692,C3270,A6770,C0330] GO : microvillus assembly GO : luteinization GO : immune response-activating cell surface receptor signaling pathway GO : protein autophosphorylation GO : oxygen transporter activity GO : molecular function GO : positive regulation of protein ubiquitination GO : membrane part GO : DNA repair 13

14 GO : response to organic substance GO : response to cold GO : regulation of leukocyte mediated cytotoxicity This tree elucidates two interesting outcomes where the bacterial load is reduced while nothing happens to the host. The first outcome occurs when the oxygen transporter activity is targeted (GO ) by some of the compounds S9692, A0966 and Q3251. The second outcome occurs when DNA repair (GO ), the response to organic substance (GO ) and the response to cold (GO ) are targeted simultaneously by some of the compounds L2167, G6793 and F Mtb - discrete GO yes: GO yes: [0,0] [7.0,7.0]: 7 compound: [A2385,R5010,C7632,C9511,T9652,D7910,P9375] +--no: [-1,-1] [7.0,11.0]: no: GO yes: [1,-1] [2.0,3.0]: 3 compound: [C9911,C9754,O3125] +--no: GO yes: [0,0] [71.0,70.0]: no: GO yes: [-1,-1] [1.0,2.0]: 2 compound: [C6645,M6383] +--no: GO yes: [-1,0] [4.0,5.0]: 6 compound: [M6760,L8789,Q0125,E7881,H89,M5250] +--no: GO yes: [-1,0] [2.0,2.0]: 3 compound: [M2537,H1512,K1003] +--no: GO yes: GO yes: [-1,0] [3.0,3.0]: 3 compound: [A0966,Q3251,S9692] +--no: [0,0] [2.0,2.0]: 2 compound: [A4638,F6627] +--no: GO yes: [0,0] [91.0,93.0]: no: GO yes: [0,0] [20.0,21.0]: no: GO yes: [-1,0] [2.0,3.0]: 3 compound: [L2167,L3791,S3065] +--no: [0,0] [668.0,698.0]:

15 compound: [...] GO : melanocyte differentiation GO : endosomal transport GO : microvillus assembly GO : regulation of protein ubiquitination GO : serine-type endopeptidase inhibitor activity GO : protein kinase B signaling cascade GO : cholesterol biosynthetic process GO : oxygen transporter activity GO : two-component sensor activity GO : negative regulation of DNA replication GO : response to prostaglandin stimulus GO : ensheathment of neurons This tree illustrates four interesting outcomes where the bacterial load is reduced, while nothing happens to the host. The first outcome occurs when the protein kinase B signaling cascade (GO ) is targeted by some of the following compounds: M6760, L8789, Q0125, E7881, H89 and M5250. The second outcome occurs when the cholesterol biosynthetic process (GO ) is targeted by some of the following compounds: M2537,H1512 and K1003. The third outcome occurs when both oxygen transporter activity (GO ) and two-component sensor activity (GO ) are targeted simultaneously by some of the following compounds A0966,Q3251 and S9692. The fourth outcome occurs when the ensheathment of neurons (GO ) is targeted by some of the following compounds L2167, L3791 and S Stm - numeric GO yes: [10.795,-6.075]: 2 compound: [C9754,M1404] +--no: GO yes: [6.625,-4.105]: 4 compound: [I3766,V1377,P4405,V8879] +--no: GO yes: [3.71,-5.18]: 2 compound: [C9911,E1383] +--no: GO yes: [ , ]: no: GO yes: [2.46,-2.45]: 2 compound: [A2385,A9809] +--no: GO yes: [-3.185,0.215]: 2 compound: [H1512,F1293] +--no: [ , ]: 929 compound: [...] GO : RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription 15

16 GO : phosphate ion binding GO : regulation of double-strand break repair via homologous recombination GO : hormone-mediated signaling pathway GO : regulation of transcription by galactose GO : steroid delta-isomerase activity This tree points-out to an outcome where the bacterial load is reduced, while the host cell remains unharmed. This occurs when the steroid delta-isomerase activity (GO ) is targeted by some of the following compounds: H1512 and F Stm - discrete GO yes: GO yes: [1,-1] [4.0,4.0]: 4 compound: [C9911,V1377,P4405,V8879] +--no: GO yes: GO yes: [0,0] [2.0,2.0]: 2 compound: [A2385,R5010] +--no: [1,-1] [4.0,4.0]: 4 compound: [C9754,M1404,A9809,E1383] +--no: GO yes: [0,-1] [1.0,2.0]: 2 compound: [N3510,C7522] +--no: GO yes: [0,0] [26.0,26.0]: no: [0,-1] [2.0,2.0]: 3 compound: [B168,A8598,T7402] +--no: GO yes: GO yes: [0,0] [2.0,2.0]: 2 compound: [T1132,O3125] +--no: [1,-1] [2.0,2.0]: 2 compound: [C6645,M6383] +--no: GO yes: [0,0] [19.0,22.0]: no: GO yes: [0,-1] [1.0,1.0]: 2 compound: [P108,C5134] +--no: GO yes: [-1,0] [1.0,2.0]: 2 compound: [P8386,O8757] +--no: GO yes: [0,0] [1.0,2.0]: 2 compound: [N2255,D9766] +--no: GO yes: [0,-1] [2.0,1.0]: 2 16

17 compound: [H2380,S7690] +--no: [0,0] [878.0,872.0]: 889 compound: [...] GO : regulation of histone H3-K9 acetylation GO : regulation of chemokine biosynthetic process GO : protein acetylation GO : urea cycle GO : aggressive behavior GO : membrane part GO : serine-type endopeptidase inhibitor activity GO : MAPK cascade GO : positive regulation of translation GO : hyperosmotic salinity response GO : cytolysis by symbiont of host cells GO : uridine transport GO : protein phosphatase inhibitor activity This tree points-out to an outcome where the bacterial load is reduced, while the host cell remains unharmed. This occurs when the cytolysis by symbiont of host cells (GO ) is targeted by some of the following compounds: P8386 and O GO and KEGG terms plus interaction information Mtb - numeric GO yes: [-0.12, ]: 4 compound: [C9911,C9754,P4405,O3125] +--no: GO yes: [-0.866, ]: no: IAGO yes: [ , ]: 3 compound: [G6416,S9692,M1404] +--no: GO yes: [-2.585,-1.238]: 10 compound: [M6760,R5010,Q0125,N3510,F9397,P0453,P8139,T5575,H89,S3567] +--no: GO yes: [0.24,-4.9]: 3 compound: [C6645,T1132,M6383] +--no: GO yes: [ , ]: no: IAGO yes: [ , ]: no: [ , ]: 777 compound: [...] 17

18 GO : microvillus assembly GO : luteinization IAGO : regulation of interferon-beta biosynthetic process GO : regulation of glucose transport GO : serine-type endopeptidase inhibitor activity GO : cellular macromolecular complex subunit organization IAGO : cleavage furrow This tree presents a scenario where the bacterial load is decreased while the host is unharmed. This scenario occurs when the regulation of glucose transport (GO ) is targeted by M6760, R5010, Q0125, N3510, F9397, P0453, P8139, T5575, H89 and S Mtb - discrete IAGO yes: GO yes: [-1,-1] [5.0,7.0]: 7 compound: [C6645,V1377,P4405,P8139,V8879,C3930,M6383] +--no: [0,0] [32.0,31.0]: no: GO yes: [-1,0] [5.0,5.0]: 8 compound: [C9911,M6760,L8789,Q0125,E7881,W1628,H89,M5250] +--no: GO yes: [0,0] [23.0,20.0]: no: GO yes: [0,-1] [2.0,2.0]: 3 compound: [P0453,T9033,T182] +--no: GO yes: [0,0] [26.0,34.0]: no: GO yes: [0,-1] [3.0,2.0]: 4 compound: [Z0878,M2537,I1149,D8690] +--no: GO yes: GO yes: [-1,0] [3.0,3.0]: 3 compound: [A0966,Q3251,S9692] +--no: [0,0] [2.0,2.0]: 2 compound: [A4638,F6627] +--no: [0,0] [776.0,808.0]: 832 compound: [...] IAGO : carbohydrate derivative biosynthetic process GO : response to interferon-gamma GO : protein kinase B signaling cascade GO : bone resorption GO : melanocyte differentiation GO : DNA double-strand break processing 18

19 GO : positive regulation of striated muscle tissue development GO : oxygen transporter activity GO : two-component sensor activity This tree presents a scenario where the bacterial load is decreased while nothing happens to the host. There are two possibilities for this scenario to occur. To begin with, the protein kinase B signaling cascade (GO ) needs to be targeted by C9911, M6760, L8789, Q0125, E7881, W1628, H89 or M5250. Next, the two-component sensor activity (GO ) needs to be targeted by A0966, Q3251 or S Stm - numeric IAGO yes: [6.954,-3.874]: 5 compound: [I3766,V1377,N3510,P4405,V8879] +--no: GO yes: [10.795,-6.075]: 2 compound: [C9754,M1404] +--no: IAGO yes: [3.085,-3.815]: 4 compound: [C9911,A2385,A9809,E1383] +--no: GO yes: [2.53,-1.916]: 5 compound: [C6645,R5010,T1132,O3125,M6383] +--no: IAGO yes: GO yes: [2.07,-3.15]: 3 compound: [N1786,T182,C7522] +--no: GO yes: [-3.8,0.2]: 2 compound: [H1512,D9815] +--no: [ , ]: no: [ , ]: 899 compound: [...] IAGO : JUN kinase activity GO : RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription IAGO : branching involved in prostate gland morphogenesis GO : serine-type endopeptidase inhibitor activity IAGO : superoxide metabolic process GO : orexin receptor activity GO : negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure This tree presents an outcome where the bacterial load is decreased and nothing happens to the host. This outcome occurs when the negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO ) is targeted by H1512 or D9815, while the orexin receptor activity (GO ) is not targeted. 19

20 5.3.4 Stm - discrete IAGO yes: [0,-1] [8.0,7.0]: no: GO yes: [1,-1] [2.0,2.0]: 2 compound: [C9754,M1404] +--no: GO yes: [1,-1] [2.0,2.0]: 3 compound: [C9911,N3510,S5567] +--no: IAGO yes: [-1,0] [1.0,2.0]: 3 compound: [G0668,C8221,H89] +--no: GO yes: [0,-1] [1.0,1.0]: 2 compound: [P108,C5134] +--no: GO yes: [0,0] [29.0,28.0]: no: GO yes: [-1,0] [1.0,2.0]: 2 compound: [P8386,O8757] +--no: GO yes: [0,0] [1.0,2.0]: 2 compound: [N2255,D9766] +--no: GO yes: [0,0] [117.0,122.0]: no: GO yes: [0,-1] [2.0,1.0]: 2 compound: [C0993,S7690] +--no: [0,0] [774.0,765.0]: 777 compound: [...] IAGO : adrenal gland development GO : RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription GO : positive regulation of Notch signaling pathway IAGO : negative regulation of muscle cell apoptotic process GO : hyperosmotic salinity response GO : regulation of fatty acid beta-oxidation GO : cytolysis by symbiont of host cells GO : uridine transport GO : double-strand break repair GO : protein phosphatase type 2A regulator activity This tree presents two scenarios for decrease of bacterial load while nothing happens to the cell. The first scenario occurs when we target a protein that is in interaction with a protein involved in negative regulation of muscle cell apoptotic process (IAGO ). This occurs 20

21 when some of the following compounds are applied: G0668,C8221 and H89. The second scenario occurs when the cytolysis by symbiont of host cells (GO ) is targeted by P8386 or O