APA Result

Altered Pathway Analyzer

Dataset

Control expression matrix: sample/control.txt

Disease expression matrix: sample/case.txt

Options selected:

P value threshold: 0.05

Correlation thershold: 0.1

Fold change threshold: 0

Pathway source: KEGG (database/Pathways/KEGG.txt)

Gene Regulatory source: database/GRN.ssv

Seed ID source: database/seeds.txt

Gene count threshold: 10

Only Differential Regulation: F

R path: /home/abhinav/R/R-3.3.1/bin/Rscript

Include Down-regulated genes: F

Number of iterations: NULL


Result table. Click header for column-wise sorting
Pathway Rank Dy Score DR Score DP Score

●

 RENAL_CELL_CARCINOMA 0.129 0.140 0.171 0.292

●

 GLYCEROLIPID_METABOLISM 0.011 0.174 0.041 0.001

●

 RIBOSOME 0.031 0.498 0.000 0.001

●

 TYROSINE_METABOLISM 0.019 0.281 0.021 0.001

●

 PROSTATE_CANCER 0.468 0.154 0.311 1.000

●

 MTOR_SIGNALING_PATHWAY 0.068 0.147 0.158 0.465

●

 VIRAL_MYOCARDITIS 0.039 0.294 0.099 0.001

●

 APOPTOSIS 0.395 0.178 0.360 0.216

●

 CHEMOKINE_SIGNALING_PATHWAY 0.052 0.164 0.058 0.103

●

 ADHERENS_JUNCTION 0.349 0.206 0.316 0.355

●

 INOSITOL_PHOSPHATE_METABOLISM 0.002 0.144 0.000 0.125

●

 INSULIN_SIGNALING_PATHWAY 0.327 0.173 0.215 0.068

●

 FOCAL_ADHESION 0.275 0.174 0.171 0.182

●

 GLYCEROPHOSPHOLIPID_METABOLISM 0.010 0.219 0.018 0.001

●

 PEROXISOME 0.000 0.121 0.000 0.156

●

 LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION 0.051 0.151 0.098 0.156

●

 RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY 0.066 0.258 0.164 0.001

●

 TRYPTOPHAN_METABOLISM 0.029 0.465 0.000 0.001

●

 NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION 0.011 0.210 0.025 0.001

●

 VASOPRESSIN_REGULATED_WATER_REABSORPTION 0.049 0.255 0.091 0.001

●

 ENDOCYTOSIS 0.202 0.181 0.237 0.101

●

 ACUTE_MYELOID_LEUKEMIA 0.267 0.169 0.226 0.496

●

 LYSINE_DEGRADATION 0.024 0.405 0.000 0.001

●

 PATHOGENIC_ESCHERICHIA_COLI_INFECTION 0.048 0.268 0.144 0.355

●

 CHRONIC_MYELOID_LEUKEMIA 0.209 0.162 0.225 0.546

●

 MELANOMA 0.202 0.081 0.247 0.689

●

 AMYOTROPHIC_LATERAL_SCLEROSIS_ALS 0.173 0.241 0.280 0.001

●

 JAK_STAT_SIGNALING_PATHWAY 0.496 0.185 0.246 0.102

●

 MAPK_SIGNALING_PATHWAY 0.349 0.195 0.196 0.113

●

 EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION 0.059 0.259 0.143 0.059

●

 CYTOSOLIC_DNA_SENSING_PATHWAY 0.001 0.138 0.000 0.001

●

 CELL_ADHESION_MOLECULES_CAMS 0.063 0.258 0.125 0.001

●

 RETINOL_METABOLISM 0.002 0.142 0.000 0.001

●

 PRIMARY_IMMUNODEFICIENCY 0.025 0.213 0.070 0.001

●

 WNT_SIGNALING_PATHWAY 0.288 0.163 0.228 0.211

●

 ENDOMETRIAL_CANCER 0.302 0.106 0.364 0.708

●

 FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS 0.027 0.242 0.052 0.226

●

 OLFACTORY_TRANSDUCTION 0.009 0.196 0.019 0.000

●

 LONG_TERM_POTENTIATION 0.054 0.186 0.074 0.057

●

 ERBB_SIGNALING_PATHWAY 0.045 0.098 0.093 0.248

●

 SYSTEMIC_LUPUS_ERYTHEMATOSUS 0.033 0.318 0.068 0.000

●

 COLORECTAL_CANCER 0.389 0.221 0.381 0.432

●

 HYPERTROPHIC_CARDIOMYOPATHY_HCM 0.032 0.246 0.088 0.001

●

 ALLOGRAFT_REJECTION 0.352 0.413 0.492 0.001

●

 HEMATOPOIETIC_CELL_LINEAGE 0.063 0.204 0.068 0.035

●

 PATHWAYS_IN_CANCER 1.000 0.179 0.272 0.306

●

 TYPE_II_DIABETES_MELLITUS 0.272 0.206 0.354 0.050

●

 CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION 0.295 0.193 0.174 0.053

●

 REGULATION_OF_AUTOPHAGY 0.011 0.203 0.052 0.000

●

 PURINE_METABOLISM 0.017 0.209 0.028 0.001

●

 VASCULAR_SMOOTH_MUSCLE_CONTRACTION 0.039 0.189 0.057 0.016

●

 ALZHEIMERS_DISEASE 0.193 0.203 0.186 0.001

●

 DRUG_METABOLISM_OTHER_ENZYMES 0.007 0.207 0.000 0.001

●

 PROTEASOME 0.049 0.293 0.140 0.001

●

 OOCYTE_MEIOSIS 0.122 0.188 0.155 0.041

●

 SMALL_CELL_LUNG_CANCER 0.216 0.208 0.228 0.269

●

 HUNTINGTONS_DISEASE 0.062 0.195 0.074 0.027

●

 PROGESTERONE_MEDIATED_OOCYTE_MATURATION 0.134 0.159 0.175 0.184

●

 METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 0.016 0.285 0.028 0.001

●

 AXON_GUIDANCE 0.076 0.199 0.208 0.001

●

 THYROID_CANCER 0.372 0.287 0.538 0.620

●

 LONG_TERM_DEPRESSION 0.044 0.149 0.099 0.000

●

 VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.016 0.218 0.095 0.001

●

 UBIQUITIN_MEDIATED_PROTEOLYSIS 0.120 0.183 0.197 0.060

●

 PANCREATIC_CANCER 0.282 0.122 0.282 0.849

●

 SPHINGOLIPID_METABOLISM 0.012 0.270 0.000 0.001

●

 TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY 0.047 0.165 0.087 0.068

●

 TGF_BETA_SIGNALING_PATHWAY 0.152 0.175 0.177 0.093

●

 NON_SMALL_CELL_LUNG_CANCER 0.116 0.137 0.196 0.517

●

 NOTCH_SIGNALING_PATHWAY 0.082 0.181 0.185 0.001

●

 GNRH_SIGNALING_PATHWAY 0.148 0.193 0.132 0.001

●

 ALDOSTERONE_REGULATED_SODIUM_REABSORPTION 0.056 0.256 0.107 0.249

●

 NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY 0.094 0.225 0.172 0.001

●

 CELL_CYCLE 0.263 0.211 0.220 0.602

●

 AUTOIMMUNE_THYROID_DISEASE 0.322 0.284 0.412 0.001

●

 CARDIAC_MUSCLE_CONTRACTION 0.010 0.188 0.029 0.001

●

 VEGF_SIGNALING_PATHWAY 0.164 0.263 0.228 0.187

●

 LYSOSOME 0.026 0.363 0.034 0.001

●

 FATTY_ACID_METABOLISM 0.012 0.261 0.000 0.001

●

 PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM 0.006 0.182 0.011 0.256

●

 STARCH_AND_SUCROSE_METABOLISM 0.003 0.139 0.020 0.001

●

 LEISHMANIA_INFECTION 0.092 0.224 0.144 0.000

●

 RNA_DEGRADATION 0.003 0.139 0.015 0.001

●

 GRAFT_VERSUS_HOST_DISEASE 0.342 0.912 0.414 0.000

●

 P53_SIGNALING_PATHWAY 0.400 0.155 0.398 0.517

●

 INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION 0.024 0.224 0.094 0.000

●

 ABC_TRANSPORTERS 0.004 0.167 0.000 0.001

●

 FC_EPSILON_RI_SIGNALING_PATHWAY 0.065 0.205 0.099 0.226

●

 PRION_DISEASES 0.013 0.151 0.041 0.000

●

 NEUROTROPHIN_SIGNALING_PATHWAY 0.273 0.198 0.247 0.162

●

 DRUG_METABOLISM_CYTOCHROME_P450 0.003 0.130 0.029 0.001

●

 ASTHMA 0.034 0.341 0.092 0.000

●

 TIGHT_JUNCTION 0.018 0.213 0.039 0.276

●

 PPAR_SIGNALING_PATHWAY 0.208 0.270 0.294 0.001

●

 COMPLEMENT_AND_COAGULATION_CASCADES 0.024 0.139 0.137 0.001

●

 VIBRIO_CHOLERAE_INFECTION 0.030 0.298 0.046 0.001

●

 ECM_RECEPTOR_INTERACTION 0.019 0.180 0.058 0.001

●

 PYRIMIDINE_METABOLISM 0.033 0.194 0.082 0.001

●

 GLIOMA 0.157 0.103 0.212 0.676

●

 SPLICEOSOME 0.018 0.304 0.036 0.104

●

 AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM 0.009 0.191 0.036 0.001

●

 T_CELL_RECEPTOR_SIGNALING_PATHWAY 0.154 0.232 0.174 0.144

●

 PYRUVATE_METABOLISM 0.042 0.312 0.105 0.001

●

 HEDGEHOG_SIGNALING_PATHWAY 0.090 0.144 0.175 0.001

●

 OXIDATIVE_PHOSPHORYLATION 0.010 0.230 0.013 0.001

●

 ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC 0.033 0.269 0.081 0.164

●

 NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY 0.399 0.597 0.288 0.082

●

 CALCIUM_SIGNALING_PATHWAY 0.013 0.196 0.017 0.001

●

 REGULATION_OF_ACTIN_CYTOSKELETON 0.082 0.182 0.093 0.119

●

 B_CELL_RECEPTOR_SIGNALING_PATHWAY 0.077 0.173 0.146 0.233

●

 GAP_JUNCTION 0.075 0.159 0.108 0.000

●

 PROXIMAL_TUBULE_BICARBONATE_RECLAMATION 0.015 0.285 0.011 0.000

●

 ARACHIDONIC_ACID_METABOLISM 0.052 0.273 0.119 0.001

●

 TYPE_I_DIABETES_MELLITUS 0.310 0.371 0.434 0.001

●

 PARKINSONS_DISEASE 0.028 0.181 0.090 0.001

●

 DILATED_CARDIOMYOPATHY 0.048 0.217 0.081 0.001

●

 MELANOGENESIS 0.074 0.241 0.070 0.264

●

 ADIPOCYTOKINE_SIGNALING_PATHWAY 0.128 0.182 0.211 0.138

●

 STEROID_HORMONE_BIOSYNTHESIS 0.060 0.490 0.089 0.001

●

 ARGININE_AND_PROLINE_METABOLISM 0.009 0.210 0.022 0.001

●

 ANTIGEN_PROCESSING_AND_PRESENTATION 0.071 0.774 0.050 0.000

Contact

Queries and complaints

Dr. Dinesh Gupta: dinesh@icgeb.res.in

Abhinav Kaushik: abhinav@icgeb.res.in