APA Result

Altered Pathway Analyzer

Dataset

Control expression matrix: ../sam2/control.dat

Disease expression matrix: ../sam2/case.dat

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

●

 PROXIMAL_TUBULE_BICARBONATE_RECLAMATION 0.029 0.332 0.133 0.002

●

 CARDIAC_MUSCLE_CONTRACTION 0.015 0.166 0.087 0.001

●

 BIOSYNTHESIS_OF_UNSATURATED_FATTY_ACIDS 0.018 0.273 0.059 0.000

●

 RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY 0.005 0.111 0.021 0.001

●

 SPLICEOSOME 0.011 0.274 0.000 0.001

●

 CELL_CYCLE 0.228 0.240 0.322 0.393

●

 NOTCH_SIGNALING_PATHWAY 0.161 0.221 0.300 0.002

●

 CALCIUM_SIGNALING_PATHWAY 0.117 0.236 0.213 0.085

●

 MELANOGENESIS 0.244 0.327 0.337 0.077

●

 PROPANOATE_METABOLISM 0.009 0.231 0.000 0.001

●

 CHEMOKINE_SIGNALING_PATHWAY 0.031 0.214 0.084 0.011

●

 NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION 0.013 0.124 0.062 0.001

●

 RENAL_CELL_CARCINOMA 0.107 0.081 0.235 0.001

●

 NEUROTROPHIN_SIGNALING_PATHWAY 0.038 0.188 0.093 0.043

●

 ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC 0.019 0.152 0.134 0.001

●

 PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM 0.021 0.373 0.081 0.027

●

 CELL_ADHESION_MOLECULES_CAMS 0.111 0.315 0.214 0.021

●

 COLORECTAL_CANCER 0.080 0.149 0.223 0.832

●

 NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY 0.046 0.165 0.147 0.001

●

 LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION 0.084 0.283 0.181 0.015

●

 ACUTE_MYELOID_LEUKEMIA 0.275 0.139 0.598 0.545

●

 SYSTEMIC_LUPUS_ERYTHEMATOSUS 0.017 0.117 0.088 0.000

●

 TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY 0.018 0.096 0.059 0.084

●

 ECM_RECEPTOR_INTERACTION 0.022 0.368 0.099 0.001

●

 ENDOMETRIAL_CANCER 0.490 0.209 0.709 0.899

●

 ADIPOCYTOKINE_SIGNALING_PATHWAY 0.255 0.076 0.409 0.001

●

 GLIOMA 0.263 0.194 0.503 0.500

●

 VASCULAR_SMOOTH_MUSCLE_CONTRACTION 0.026 0.241 0.098 0.001

●

 SPHINGOLIPID_METABOLISM 0.045 0.434 0.148 0.001

●

 CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION 0.160 0.258 0.189 0.346

●

 CITRATE_CYCLE_TCA_CYCLE 0.005 0.155 0.007 0.428

●

 HUNTINGTONS_DISEASE 0.029 0.200 0.044 0.105

●

 EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION 0.202 0.392 0.406 0.114

●

 HYPERTROPHIC_CARDIOMYOPATHY_HCM 0.003 0.110 0.013 0.001

●

 GLYCEROPHOSPHOLIPID_METABOLISM 0.011 0.274 0.000 0.000

●

 ADHERENS_JUNCTION 0.481 0.266 0.488 0.313

●

 ARGININE_AND_PROLINE_METABOLISM 0.115 0.241 0.375 0.001

●

 ALZHEIMERS_DISEASE 0.010 0.186 0.017 0.001

●

 PYRUVATE_METABOLISM 0.007 0.203 0.003 0.001

●

 OLFACTORY_TRANSDUCTION 0.014 0.318 0.000 0.001

●

 PEROXISOME 0.032 0.291 0.117 0.071

●

 BUTANOATE_METABOLISM 0.047 0.402 0.166 0.001

●

 VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.037 0.218 0.170 0.001

●

 COMPLEMENT_AND_COAGULATION_CASCADES 0.047 0.405 0.166 0.001

●

 GNRH_SIGNALING_PATHWAY 0.202 0.123 0.352 0.154

●

 PATHOGENIC_ESCHERICHIA_COLI_INFECTION 0.088 0.283 0.448 0.101

●

 ERBB_SIGNALING_PATHWAY 0.475 0.186 0.590 0.429

●

 GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.086 0.362 0.612 0.001

●

 DILATED_CARDIOMYOPATHY 0.004 0.123 0.011 0.000

●

 VIRAL_MYOCARDITIS 0.011 0.265 0.011 0.002

●

 FC_EPSILON_RI_SIGNALING_PATHWAY 0.036 0.148 0.143 0.144

●

 MAPK_SIGNALING_PATHWAY 0.156 0.186 0.189 0.223

●

 BLADDER_CANCER 0.378 0.321 0.583 0.571

●

 LONG_TERM_DEPRESSION 0.023 0.164 0.164 0.000

●

 TRYPTOPHAN_METABOLISM 0.052 0.249 0.378 0.001

●

 VEGF_SIGNALING_PATHWAY 0.015 0.077 0.133 0.001

●

 OOCYTE_MEIOSIS 0.042 0.226 0.120 0.235

●

 LEISHMANIA_INFECTION 0.093 0.143 0.262 0.001

●

 GAP_JUNCTION 0.264 0.193 0.505 0.297

●

 LONG_TERM_POTENTIATION 0.041 0.238 0.113 0.001

●

 NITROGEN_METABOLISM 0.016 0.358 0.000 0.001

●

 RETINOL_METABOLISM 0.004 0.157 0.000 0.001

●

 TGF_BETA_SIGNALING_PATHWAY 0.100 0.325 0.168 0.116

●

 B_CELL_RECEPTOR_SIGNALING_PATHWAY 0.023 0.162 0.108 0.001

●

 PROSTATE_CANCER 0.771 0.204 0.612 0.839

●

 BASAL_CELL_CARCINOMA 0.063 0.196 0.249 0.183

●

 PYRIMIDINE_METABOLISM 0.008 0.140 0.084 0.001

●

 AXON_GUIDANCE 0.017 0.251 0.044 0.001

●

 ALDOSTERONE_REGULATED_SODIUM_REABSORPTION 0.219 0.524 0.380 0.002

●

 LYSOSOME 0.071 0.563 0.095 0.000

●

 ABC_TRANSPORTERS 0.017 0.372 0.000 0.000

●

 METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 0.015 0.347 0.000 0.002

●

 REGULATION_OF_ACTIN_CYTOSKELETON 0.110 0.206 0.201 0.250

●

 T_CELL_RECEPTOR_SIGNALING_PATHWAY 0.032 0.132 0.103 0.001

●

 FOCAL_ADHESION 0.320 0.262 0.341 0.138

●

 PARKINSONS_DISEASE 0.011 0.240 0.019 0.000

●

 TYROSINE_METABOLISM 0.178 0.418 0.701 0.001

●

 ANTIGEN_PROCESSING_AND_PRESENTATION 0.007 0.198 0.000 0.000

●

 APOPTOSIS 0.050 0.110 0.121 0.154

●

 PANCREATIC_CANCER 0.338 0.121 0.592 0.666

●

 NON_SMALL_CELL_LUNG_CANCER 0.463 0.245 0.666 0.267

●

 HEMATOPOIETIC_CELL_LINEAGE 0.109 0.141 0.266 0.068

●

 ARACHIDONIC_ACID_METABOLISM 0.027 0.393 0.082 0.002

●

 TERPENOID_BACKBONE_BIOSYNTHESIS 0.042 0.325 0.251 0.001

●

 OXIDATIVE_PHOSPHORYLATION 0.012 0.289 0.000 0.000

●

 LYSINE_DEGRADATION 0.011 0.269 0.000 0.250

●

 STEROID_HORMONE_BIOSYNTHESIS 0.037 0.496 0.120 0.001

●

 WNT_SIGNALING_PATHWAY 0.220 0.272 0.263 0.080

●

 JAK_STAT_SIGNALING_PATHWAY 0.091 0.227 0.163 0.141

●

 TIGHT_JUNCTION 0.032 0.307 0.111 0.011

●

 FATTY_ACID_METABOLISM 0.038 0.235 0.169 0.001

●

 INOSITOL_PHOSPHATE_METABOLISM 0.017 0.385 0.000 0.000

●

 RIBOSOME -0.000 0.080 0.000 0.167

●

 PROGESTERONE_MEDIATED_OOCYTE_MATURATION 0.005 0.143 0.027 0.000

●

 PPAR_SIGNALING_PATHWAY 0.248 0.238 0.421 0.001

●

 INSULIN_SIGNALING_PATHWAY 0.033 0.129 0.060 0.001

●

 ENDOCYTOSIS 0.095 0.206 0.193 0.175

●

 UBIQUITIN_MEDIATED_PROTEOLYSIS 0.015 0.111 0.119 0.059

●

 P53_SIGNALING_PATHWAY 0.101 0.226 0.232 0.063

●

 SMALL_CELL_LUNG_CANCER 0.022 0.235 0.077 0.223

●

 GLYCEROLIPID_METABOLISM 0.014 0.325 0.000 0.001

●

 HISTIDINE_METABOLISM 0.053 0.360 0.328 0.001

●

 PURINE_METABOLISM 0.008 0.184 0.035 0.000

●

 MELANOMA 0.382 0.220 0.731 0.599

●

 PATHWAYS_IN_CANCER 1.000 0.233 0.437 0.362

●

 GLUTATHIONE_METABOLISM 0.010 0.259 0.000 0.044

●

 MTOR_SIGNALING_PATHWAY 0.003 0.107 0.029 0.001

●

 VIBRIO_CHOLERAE_INFECTION 0.046 0.503 0.194 0.000

●

 DRUG_METABOLISM_CYTOCHROME_P450 0.043 0.328 0.252 0.001

●

 FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS 0.021 0.228 0.114 0.022

●

 AMYOTROPHIC_LATERAL_SCLEROSIS_ALS 0.025 0.178 0.085 0.001

Contact

Queries and complaints

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

Abhinav Kaushik: abhinav@icgeb.res.in