Spreadsheet: a6c4f91d-82c3-4376-a485-f587b3122bb4
Sheet: Sheet1

Table S4 - Autophagy | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | Unnamed: 13 | Unnamed: 14 | Unnamed: 15 | Unnamed: 16 | Unnamed: 17 | Control vs PDK13 | Unnamed: 19 | Unnamed: 20 | Unnamed: 21 | Unnamed: 22 | Unnamed: 23 | Unnamed: 24
 |  |  |  |  |  |  |  |  |  |  | ln(fold change) |  |  |  | sqrt(JS) |  |  | ln(fold change) |  |  |  | sqrt(JS)
Hugo name | Microarray | DENV screen ([NAME]) | DENV screen (Dm) | YFV screen | WNV screen (Published) | WNV screen (Unpublished) | HCV-virus screen | HCV-replicon screen | DENV UTR-BP's | DENV-Y2H | Gene | Isoform | CDS | TSS | Splicing | Promoter | CDS | Gene | Isoform | CDS | TSS | Splicing | Promoter | CDS
AKT1S1 |  | present |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
[NAME] |  |  |  |  |  |  |  |  |  |  | na | TCONS_00047713:-1.10265 | na | na | na | na | na | XLOC_013754:-0.817218, XLOC_014911:0.529833 | TCONS_00047713:-2.01942, TCONS_00055361:1.47376, TCONS_00058783:-0.757634, TCONS_00059038:0.882352, TCONS_00059039:1.23758 | na | na | na | na | na
ATG10 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
ATG12 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | TCONS_00251353:1.87064 | na | na | na | na | na
[NAME] |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
ATG14 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
ATG16L1 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | TCONS_00160054:1.16536, TCONS_00160056:2.64908 | na | na | na | na | na
ATG2A |  |  |  |  |  |  |  |  |  |  | na | TCONS_00057788:-1.80584, TCONS_00057790:2.16905 | na | na | na | na | na | na | TCONS_00050879:1.79769e+308, TCONS_00050880:-1.79769e+308, TCONS_00057789:1.8887 | na | na | na | na | na
ATG2B |  |  |  |  |  |  |  |  |  |  | na | TCONS_00087193:2.15708 | na | na | na | na | na | XLOC_026841:0.729785 | TCONS_00087193:2.41564, TCONS_00087196:1.70547, TCONS_00089479:-1.79769e+308 | na | na | na | na | na
[NAME] |  |  |  |  |  |  |  |  |  |  | na | TCONS_00224315:-2.28835, TCONS_00227679:-1.79769e+308 | na | TSS64413:-1.79769e+308, TSS64414:-2.28835 | na | XLOC_064302:0.28563 | na | XLOC_064302:0.476954 | TCONS_00221020:1.52526, TCONS_00227679:-1.79769e+308 | na | TSS64413:-1.79769e+308, TSS64415:1.52526 | na | XLOC_064302:0.290043 | na
ATG4A |  |  |  |  |  |  |  |  |  |  | na | TCONS_00334256:-4.28999 | na | na | na | na | na | XLOC_103514:1.98344 | TCONS_00342504:1.98344 | na | na | na | na | na
ATG4B |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | TCONS_00160552:-1.79769e+308, TCONS_00160555:1.93454, TCONS_00160562:2.23417 | na | na | na | na | na
ATG4C |  |  |  |  |  |  |  |  |  |  | na | [NAME] | na | TSS2084:-2.25122 | na | XLOC_000900:0.207019 | na | na | na | na | na | TSS2085:0.175454 | XLOC_000900:0.186164 | na
ATG4D |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
ATG5 |  | present |  |  |  |  |  |  |  |  | na | TCONS_00276512:-3.48757 | na | na | na | na | na | na | TCONS_00268137:1.73355, TCONS_00276512:-1.62928 | na | na | na | na | na
ATG7 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
ATG9A |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
ATG9B |  |  |  |  |  |  |  |  |  |  | na | TCONS_00288165:-2.57198 | na | TSS87769:-2.57198 | TSS87764:0.832555, TSS87763:0.366799 | XLOC_087149:0.229945 | na | na | TCONS_00288153:-4.43944, TCONS_00288157:-1.79769e+308, TCONS_00288159:-0.558948, TCONS_00288163:1.79769e+308 | na | TSS87760:-4.43944, TSS87764:-1.79769e+308, TSS87766:-0.558948, TSS87769:-3.87809 | TSS87769:0.832555, TSS87763:0.309374 | XLOC_087149:0.528996 | na
BCL2 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
BECN1 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
C12orf44 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
DDIT3 | present |  |  |  |  |  |  |  |  |  | XLOC_019809:1.55027 | TCONS_00066000:1.55027 | na | na | na | na | na | XLOC_019809:2.64224 | TCONS_00066000:2.64224 | na | na | na | na | na
GABARAP | present |  |  |  |  |  |  |  |  |  | na | na | na | na | TSS35519:0.0537948 | [NAME] | na | na | na | na | na | TSS35519:0.0392364 | XLOC_036801:0.0385457 | na
[NAME] |  |  |  |  |  |  |  |  |  |  | na | TCONS_00110067:2.531 | na | na | TSS31424:0.11487 | na | na | na | TCONS_00110067:2.00544 | na | na | TSS31424:0.0794438 | na | na
KIAA0226 |  |  |  |  |  |  |  |  |  |  | XLOC_068586:-0.229398 | TCONS_00222282:1.79769e+308, TCONS_00226226:-1.79769e+308 | na | na | na | na | na | na | na | na | na | na | na | na
LAMP1 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | TSS24297:0.0985156 | XLOC_023665:0.05135 | na | na | TCONS_00078639:-1.34565 | na | TSS24301:-1.34565 | TSS24297:0.0506363 | XLOC_023665:0.094326 | na
MAP1LC3A |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | XLOC_055359:0.224709 | na | na | na | na | TSS52585:2.17497 | na | XLOC_055359:0.190186 | na
MTOR | present |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
PIK3C3 |  |  |  |  |  |  |  |  |  |  | na | TCONS_00131470:1.60731, TCONS_00135080:1.92448 | na | na | na | na | na | XLOC_040567:0.574728 | TCONS_00131469:-1.70953, TCONS_00131470:2.55249, TCONS_00135080:3.41156, TCONS_00135433:2.56007, TCONS_00135741:1.66218 | na | na | na | na | na
PIK3R4 |  |  |  |  |  |  |  |  |  |  | na | TCONS_00214060:1.80887, TCONS_00221058:2.83548, TCONS_00222796:1.79769e+308 | na | TSS64929:1.80887, TSS64933:1.79769e+308, TSS64934:2.83548 | na | XLOC_064477:0.364531 | na | na | TCONS_00214058:-1.79769e+308, TCONS_00214060:2.27349, TCONS_00221057:-1.79769e+308, TCONS_00221058:1.89414, TCONS_00222796:1.79769e+308 | na | TSS64931:-1.79769e+308, [NAME], TSS64933:1.79769e+308, TSS64934:1.89414 | TSS64927:0.241851 | XLOC_064477:0.342842 | na
RB1CC1 |  |  |  |  |  | present |  |  |  |  | na | TCONS_00300661:2.38506, TCONS_00300662:1.79769e+308, [NAME], TCONS_00307424:2.02943 | na | na | na | na | na | XLOC_091327:1.2876 | TCONS_00302909:1.69583, TCONS_00304009:1.48515, TCONS_00304010:1.33967, TCONS_00308182:1.11591 | na | na | na | na | na
RPTOR |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
ULK1 |  |  |  |  |  | present |  |  |  |  | na | TCONS_00068459:2.23289 | na | na | na | na | na | na | TCONS_00068459:2.4913, TCONS_00076761:1.79769e+308 | na | na | na | na | na
ULK2 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
UVRAG |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | XLOC_014166:0.763553 | na | na | na | na | na | na
VMP1 | present |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | na | na | na | na | na | na
WIPI1 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | XLOC_037620:0.678096 | TCONS_00120766:1.06881 | na | na | na | na | na
WIPI2 |  |  |  |  |  |  |  |  |  |  | na | TCONS_00278715:2.91106 | na | na | TSS81954:0.137223, TSS81956:0.0387532 | XLOC_084397:0.0911639 | na | na | na | na | na | TSS81954:0.151096, TSS81956:0.0454807 | XLOC_084397:0.0560315 | na
ZFYVE1 |  |  |  |  |  |  |  |  |  |  | na | na | na | na | na | na | na | na | TCONS_00086869:2.0799 | na | TSS27129:2.0799 | [NAME] | XLOC_026697:0.10514 | na
References
10. [NAME], Ng A, Sukumaran B, Gilfoy FD, Uchil PD, et [NAME]. (2008) RNA interference screen for human genes associated with West Nile virus infection. Nature 455: 242-245.
11. Sessions OM, [NAME], [NAME], Robinson TJ, Hershey CL, et [NAME]. (2009) Discovery of insect and human dengue virus host factors. Nature 458: 1047-1050.
12. [NAME], Kennel A, Deauvieau F, [NAME] R, Arnaud-Barbe N, et [NAME]. (2011) Different innate signatures induced in human monocyte-derived dendritic cells by wild-type dengue 3 virus, attenuated but reactogenic dengue 3 vaccine virus, or attenuated nonreactogenic dengue 1-4 vaccine virus strains. The Journal of infectious diseases 203: 103-108.
13. Becerra A, [NAME], [NAME], Xhaja K, de Bosch N, et [NAME]. (2009) Gene expression profiling of dengue infected human primary cells identifies secreted mediators in vivo. Journal of medical virology 81: 1403-1411.
14. [NAME], El-Bacha T, [NAME], Coello G, [NAME], et [NAME]. (2010) Gene expression analysis during dengue virus infection in HepG2 cells reveals virus control of innate immune response. The Journal of infection 60: 65-75.
15. Fink J, Gu F, [NAME], Tolfvenstam T, [NAME], et [NAME]. (2007) Host gene expression profiling of dengue virus infection in cell lines and patients. [NAME] Negl Trop Dis 1: e86.
16. [NAME], [NAME], [NAME], [NAME], [NAME], et [NAME]. (2010) The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults. Journal of virology 84: 12982-12994.
17. [NAME], Chow VT (2006) [NAME] and real-time RT-PCR analyses of a novel set of differentially expressed human genes in ECV304 endothelial-like cells infected with dengue virus type 2. Journal of virological methods 131: 47-57.
18. Loke P, [NAME], [NAME], [NAME], Batra S, et [NAME]. (2010) Gene expression patterns of dengue virus-infected children from nicaragua reveal a distinct signature of increased metabolism. [NAME] Negl Trop Dis 4: e710.
19. Long HT, [NAME], [NAME], [NAME], [NAME] T, et [NAME]. (2009) Patterns of gene transcript abundance in the blood of children with severe or uncomplicated dengue highlight differences in disease evolution and host response to dengue virus infection. J Infect Dis 199: 537-546.
20. [NAME], Romano M, Legorreta-Herrera M, Sanchez-Garcia FJ, [NAME] (2004) Gene expression in human macrophages infected with dengue virus serotype-2. Scandinavian journal of immunology 60: 631-638.
21. Nascimento EJ, [NAME] Calzavara-Silva CE, [NAME], Abath FG, et [NAME]. (2009) Gene expression profiling during early acute febrile stage of dengue infection can predict the disease outcome. PloS one 4: e7892.
22. Nasirudeen AM, [NAME] (2009) Gene expression profiling by microarray analysis reveals an important role for caspase-1 in dengue virus-induced p53-mediated apoptosis. Journal of medical virology 81: 1069-1081.
23. [NAME], [NAME], Delfraro A, [NAME], Coluchi N, et [NAME]. (2011) Dengue virus type 3 isolated from a fatal case with visceral complications induces enhanced proinflammatory responses and apoptosis of human dendritic cells. Journal of virology 85: 5374-5383.
24. [NAME], Popper S, Dolocek C, Chau TN, [NAME], et [NAME]. (2007) Patterns of host genome-wide gene transcript abundance in the peripheral blood of patients with acute dengue hemorrhagic fever. J Infect Dis 195: 1097-1107.
25. [NAME] T, [NAME], [NAME], [NAME], Chow A, et [NAME]. (2011) Characterization of early host responses in adults with dengue disease. BMC infectious diseases 11: 209.
26. [NAME], Masrinoul P, [NAME], Kalayanarooj S, Charoensirisuthikul T, et [NAME]. (2008) Differences in global gene expression in peripheral blood mononuclear cells indicate a significant role of the innate responses in progression of dengue fever but not dengue hemorrhagic fever. J Infect Dis 197: 1459-1467.
27. Umareddy I, Pluquet O, [NAME], [NAME], Chevet E, et [NAME]. (2007) Dengue virus serotype infection specifies the activation of the unfolded protein response. [NAME] 91.
28. [NAME], [NAME], [NAME], Santoro AB, Da Poian AT, et [NAME]. (2009) Dengue virus-induced regulation of the host cell translational machinery. Brazilian journal of medical and biological research : [NAME] / Sociedade [NAME]  [et al] 42: 1020-1026.
29. [NAME], [NAME], [NAME], [NAME], Shaw SK, et [NAME]. (2003) Dengue virus induces novel changes in gene expression of human umbilical vein endothelial cells. J [NAME] 77: 11822-11832.
44. Jamison SF (Unpublished) DENV Screen Human.
45. Le Breton M, Meyniel-Schicklin L, Deloire A, Coutard B, Canard B, et [NAME]. (2011) Flavivirus NS3 and NS5 proteins interaction network: a high-throughput yeast two-hybrid screen. BMC Microbiol 11: 234.
46. [NAME], [NAME], N.J., [NAME], M.A. (Unpublished) YFV Screen.
47. [NAME], [NAME], Ng A, Hu Z, [NAME], et [NAME]. (2009) A genome-wide genetic screen for host factors required for hepatitis C virus propagation. Proceedings of the National Academy of Sciences of the United States of America 106: 16410-16415.
48. [NAME], Benita Y, [NAME], [NAME], Sakamoto N, et [NAME]. (2009) A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell host & microbe 5: 298-307.
49. Ward AM, [NAME], [NAME], [NAME], [NAME], et [NAME]. (2011) Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase [NAME] binds the DB1 and DB2 3' UTR structures. RNA Biol 8: 1173-1186.