SUPPLEMENTARY FILE
GSEA analysis of 28 important autophagy genes – Complete table
Gene Upregulated gene-sets in AA
No. of enriched
genes
FDR q-val
Downregulated gene-sets in AA
No. of enriched
genes
FDR q-val
VPS15 UPREG 0 gene-sets DOWNREG 6 gene-sets
- DAZARD_RESPONSE_T
O_UV_NHEK_DN 253 0.036 V$CETS1P54_01 177 0.030 V$E2F1_Q4_01 163 0.000 V$E2F_Q3_01 167 0.000 V$E2F_Q4_01 169 0.000
V$TEL2_Q6 156 0.022
VPS34 UPREG 0 gene-sets DOWNREG 3 gene-sets
-
AGUIRRE_PANCREATI C_CANCER_COPY_NU MBER_DN
228 0.035
DAIRKEE_TERT_TARG
ETS_UP 308 0.020
DAZARD_RESPONSE_T
O_UV_NHEK_DN 253 0.036
FIP200 UPREG 1 gene-sets DOWNREG 3 gene-sets
FARMER_BREAST_CA
NCER_CLUSTER_2 33 0.000
GCACTTT,MIR-17- 5P,MIR-20A,MIR- 106A,MIR-106B,MIR- 20B,MIR-519D
492 0.030
TCCCRNNRTGC_UNKN
OWN 131 0.000
V$E2F1_Q6_01 175 0.000
ATG03 UPREG 0 gene-sets DOWNREG 0 gene-sets
- -
ATG04A UPREG 0 gene-sets DOWNREG 0 gene-sets
- -
ATG04B UPREG 0 gene-sets DOWNREG 1 gene-sets
-
BARRIER_CANCER_RE LAPSE_NORMAL_SAM
PLE_DN
30 0.043
ATG05 UPREG 0 gene-sets DOWNREG 1 gene-sets
-
AGUIRRE_PANCREATI C_CANCER_COPY_NU
MBER_DN
228 0.035
ATG07 UPREG 0 gene-sets DOWNREG 1 gene-sets
-
POSITIVE_REGULATIO N_OF_METABOLIC_PR OCESS
221 0.046
ATG10 UPREG 0 gene-sets DOWNREG 1 gene-sets
- WANG_LMO4_TARGET
S_UP 328 0.20
ATG12 UPREG 0 gene-sets DOWNREG 0 gene-sets
- -
ATG13b UPREG 0 gene-sets DOWNREG 1 gene-sets
- WANG_CLIM2_TARGE
TS_UP 209 0.024
ATG14 UPREG 0 gene-sets DOWNREG 0 gene-sets
- -
ATG16L
1 UPREG 0 gene-sets DOWNREG 3 gene-sets
- CTCTGGA,MIR-
520A,MIR-525 130 0.011 GCACTTT,MIR-17-
5P,MIR-20A,MIR-
492 0.030
106A,MIR-1 MIR-106B,MIR- 20B,MIR-519D
GTGCCAA,MIR-96 266 0.047
BECN1 UPREG 0 gene-sets DOWNREG 4 gene-sets
- GTGACGY_V$E4F1_Q6 468 0.043
HSIAO_HOUSEKEEPIN
G_GENES 377 0.032
V$ZIC3_01 199 0.031
YAO_TEMPORAL_RES PONSE_TO_PROGESTE RONE_CL
NE_CLUSTER_11
94 0.000
GABAR
APL1 UPREG 0 gene-sets DOWNREG 3 gene-sets
-
CONCANNON_APOPTO SIS_BY_EPOXOMICIN_
UP
224 0.021
DACOSTA_UV_RESPO
NSE_VIA_ERCC3_UP 298 0.006 OSMAN_BLADDER_CA
NCER_DN 355 0.003
IRGM1 UPREG 1 gene-sets DOWNREG 1 gene-sets
ICHIBA_GRAFT_VERS US_HOST_DISEASE_D 7_UP
107 0.022 BERENJENO_TRANSFO
RMED_BY_RHOA_UP 495 0.006
IRGM2 UPREG 1 gene-sets DOWNREG 0 gene-sets
ICHIBA_GRAFT_VERS US_HOST_DISEASE_D 7_UP
107 0.022 -
LAMP2 UPREG 0 gene-sets DOWNREG 11 gene-sets
- CREIGHTON_ENDOCRI
NE_THERAPY_RESIST
484 0.016
ANCE_1
CREIGHTON_ENDOCRI NE_THERAPY_RESIST ANCE_4
281 0.032
FLECHNER_PBL_KIDN EY_TRANSPLANT_OK_
VS_DON S_DONOR_UP
145 0.019
GAZDA_DIAMOND_BL ACKFAN_ANEMIA_PR OGENITOR
NITOR_DN
60 0.02
GTGCCAA,MIR-96 266 0.047 TOOKER_GEMCITABIN
E_RESISTANCE_DN 121 0.038 V$COUP_DR1_Q6 179 0.008
V$DR1_Q3 177 0.019
V$HNF4_DR1_Q3 191 0.019 V$PPAR_DR1_Q2 183 0.029
V$SP3_Q3 184 0.001
LC3A UPREG 1 gene-sets DOWNREG 7 gene-sets
BOYLAN_MULTIPLE_
MYELOMA_C_D_DN 253 0.036 GTGACGY_V$E4F1_Q6 468 0.043 LUND_SILENCED_BY_
METHYLATION 15 0.049
V$AP2ALPHA_01 174 0.030
V$ATF4_Q2 188 0.019
V$ATF_01 199 0.027
V$CREB_02 187 0.044
V$OLF1_01 199 0.035
LC3B UPREG 0 gene-sets DOWNREG 2 gene-sets
-
CONCANNON_APOPTO SIS_BY_EPOXOMICIN_
UP
224 0.021
NIKOLSKY_BREAST_C ANCER_16Q24_AMPLIC ON
46 0.030
RAB7A UPREG 0 gene-sets DOWNREG 0 gene-sets
- -
UVRAG UPREG 0 gene-sets DOWNREG 5 gene-sets
- CTCAGGG,MIR-
125B,MIR-125A 277 0.037 DNA_METABOLIC_PR
OCESS 248 0.035
GEORGES_CELL_CYCL
E_MIR192_TARGETS 58 0.015
V$MYC_Q2 132 0.044
V$MYCMAX_02 197 0.014
NOD2 UPREG 0 gene-sets DOWNREG 0 gene-sets
- -
XBP1 UPREG 0 gene-sets DOWNREG 8 gene-sets
-
CHARAFE_BREAST_CA NCER_LUMINAL_VS_B
ASAL_UP 350 0.036
GAGCTGG,MIR-337
135 0.006 GTGACGY_V$E4F1_Q6
468 0.043 HSIAO_HOUSEKEEPIN
G_GENES 377 0.032
PASQUALUCCI_LYMP HOMA_BY_GC_STAGE
_UP 262 0.027
PENG_RAPAMYCIN_RE
SPONSE_DN 67 0.001
PENG_GLUTAMINE_DE
PRIVATION_DN 82 0.009
SMITH_TERT_TARGET
S_UP 126 0.016
LRRK2 UPREG 1 gene-sets DOWNREG 0 gene-sets
SABATES_COLORECT
AL_ADENOMA_DN 260 0.016 - - -
ULK1 UPREG 0 gene-sets DOWNREG 7 gene-sets
-
CHARAFE_BREAST_CA NCER_LUMINAL_VS_B ASAL_UP
350 0.036
DEBIASI_APOPTOSIS_
BY_REOVIRUS_INFECT ION_DN
220 0.001
DOUGLAS_BMI1_TARG
ETS_UP 491 0.009
GCACTTT,MIR-17- 5P,MIR-20A,MIR- 106A,MIR-106B,MIR- 20B,MIR-519D
492 0.030
GRADE_COLON_VS_R
ECTAL_CANCER_DN 39 0.026 RASHI_RESPONSE_TO_
IONIZING_RADIATION _3
45 0.009
STEIN_ESRRA_TARGE TS_RESPONSIVE_TO_E STROGEN_DN
41 0.032
ULK2 UPREG 0 gene-sets DOWNREG 3 gene-sets
-
AMUNDSON_POOR_SU RVIVAL_AFTER_GAM MA_RADIA
150 0.019
RADIATION_2G
GGCAGCT,MIR-22 193 0.032 YGCGYRCGC_UNKNO
WN 211 0.018
PTPN2 UPREG 0 gene-sets DOWNREG 3 gene-sets
- RAMALHO_STEMNESS
_UP 197 0.008
V$NRF1_Q6 158 0.019
VANHARANTA_UTERI NE_FIBROID_WITH_7Q _DELETION_UP
67 0.010
TOTAL UPREG 5 gene-sets DOWNREG 74 gene-sets
GSEA was used to analyse the differential regulation of gene-sets associated with 28 key genes involved in autophagy. The gene set groups chosen for further evaluation had stringent cut-off values (FDR < 5 % and pValue = 0.001). While 74 gene-sets associated with autophagy genes were downregulated in the AA group, only 5 were upregulated. AA, Appendicitis and appendectomy group; UPREG “n” gene-sets, Upregulated number of gene- sets pertaining to that gene; DOWNREG “n” gene-sets, Downregulated number of gene-sets pertaining to that gene; No. of enriched genes in gene-set, the number of genes in each gene set enriched by GSEA pertaining to AA mice in this study; NOM p-val, Nominal p-value statistic; FDR q-val, false discovery rate q-value statistic; GSEA, gene set enrichment analysis.
