I have found that numbers in scientific notation (e.g 9.8E-9) are incorrectly sorted or filtered by Galaxy. Looks like the negative exponent is ignored and so if you sorting something like P values (see example below) then you find these ordered above P=1 instead at the other end of the list where P is near zero. In the example below a KEGG list is ordered on column 5 in asending order by galaxy. If you scroll to the bottom of the list, however, you will see the smallest numbers all of which are in scientific notation. I should note that I can can copy this into excel and excel will properly sort scientific notation. So this seems to be a specific problem with Galaxy. I found this problem with both filtering and sorting functions of Galaxy. Doug Cavener
41 0.53 26 1.0 0.0000025 cfa04146=Peroxisome 39 0.53 25 1.0 0.0000038 cfa04640=Hematopoietic cell lineage 29 0.59 13 1.0 0.0000044 cfa00980=Metabolism of xenobiotics by cytochrome P450 22 0.63 10 1.0 0.000016 cfa00140=Steroid hormone biosynthesis 28 0.56 19 1.0 0.000027 cfa05204=Chemical carcinogenesis 11 0.85 3 1.0 0.000033 cfa00511=Other glycan degradation 25 0.57 16 1.0 0.000052 cfa00600=Sphingolipid metabolism 9 0.90 2 1.0 0.000074 cfa00740=Riboflavin metabolism 23 0.58 14 1.0 0.000079 cfa00380=Tryptophan metabolism 15 0.68 6 1.0 0.000096 cfa04977=Vitamin digestion and absorption 22 0.56 17 1.0 0.00017 cfa00071=Fatty acid metabolism 22 0.56 17 1.0 0.00017 cfa05150=Staphylococcus aureus infection 26 0.53 27 1.0 0.00017 cfa00982=Drug metabolism - cytochrome P450 49 0.44 42 1.0 0.00018 cfa04142=Lysosome 56 0.42 47 1.0 0.00024 cfa04630=Jak-STAT signaling pathway 34 0.48 35 1.0 0.00026 cfa03320=PPAR signaling pathway 13 0.68 5 1.0 0.00027 cfa00531=Glycosaminoglycan degradation 20 0.56 21 1.0 0.00043 cfa04975=Fat digestion and absorption 22 0.54 24 1.0 0.00043 cfa00830=Retinol metabolism 19 0.56 20 1.0 0.00053 cfa00565=Ether lipid metabolism 14 0.61 11 1.0 0.00092 cfa00591=Linoleic acid metabolism 20 0.53 28 1.0 0.0011 cfa02010=ABC transporters 22 0.50 32 1.0 0.0015 cfa00280=Valine, leucine and isoleucine degradation 33 0.44 44 1.0 0.0020 cfa04974=Protein digestion and absorption 15 0.56 21 1.0 0.0022 cfa03440=Homologous recombination 14 0.56 19 1.0 0.0028 cfa00650=Butanoate metabolism 35 0.42 48 1.0 0.0035 cfa05323=Rheumatoid arthritis 16 0.52 31 1.0 0.0043 cfa00350=Tyrosine metabolism 16 0.52 31 1.0 0.0043 cfa05320=Autoimmune thyroid disease 12 0.57 15 1.0 0.0044 cfa00592=alpha-Linolenic acid metabolism 15 0.52 30 1.0 0.0054 cfa00760=Nicotinate and nicotinamide metabolism 21 0.47 39 1.0 0.0054 cfa05144=Malaria 84 0.36 66 1.0 0.0059 cfa04080=Neuroactive ligand-receptor interaction 16 0.48 33 1.0 0.0091 cfa05143=African trypanosomiasis 12 0.52 29 1.0 0.011 cfa00340=Histidine metabolism 14 0.48 34 0.99 0.015 cfa05330=Allograft rejection 9 0.56 18 1.0 0.015 cfa04614=Renin-angiotensin system 3 1.0 1 1.0 0.021 cfa00780=Biotin metabolism 35 0.38 56 0.99 0.021 cfa00240=Pyrimidine metabolism 15 0.44 43 0.99 0.030 cfa04940=Type I diabetes mellitus 11 0.48 36 0.99 0.032 cfa00563=Glycosylphosphatidylinositol(GPI)-anchor biosynthesis 29 0.38 54 0.98 0.032 cfa04512=ECM-receptor interaction 20 0.41 50 0.98 0.034 cfa04622=RIG-I-like receptor signaling pathway 9 0.50 32 0.99 0.037 cfa00100=Steroid biosynthesis 10 0.48 37 0.99 0.042 cfa04950=Maturity onset diabetes of the young 7 0.54 23 0.99 0.042 cfa03450=Non-homologous end-joining 6 0.55 22 0.99 0.055 cfa00430=Taurine and hypotaurine metabolism 6 0.55 22 0.99 0.055 cfa00790=Folate biosynthesis 22 0.38 58 0.97 0.060 cfa05140=Leishmaniasis 12 0.43 46 0.97 0.062 cfa00512=Mucin type O-Glycan biosynthesis 3 0.75 4 0.99 0.068 cfa00061=Fatty acid biosynthesis 3 0.75 4 0.99 0.068 cfa00232=Caffeine metabolism 23 0.37 62 0.96 0.070 cfa04115=p53 signaling pathway 29 0.36 64 0.96 0.071 cfa00564=Glycerophospholipid metabolism 8 0.47 38 0.98 0.071 cfa00120=Primary bile acid biosynthesis 20 0.38 59 0.96 0.074 cfa00561=Glycerolipid metabolism 19 0.38 57 0.96 0.076 cfa04612=Antigen processing and presentation 48 0.34 74 0.95 0.076 cfa05152=Tuberculosis 18 0.38 53 0.96 0.077 cfa00510=N-Glycan biosynthesis 2 1.0 1 1.0 0.077 cfa00290=Valine, leucine and isoleucine biosynthesis 16 0.39 52 0.96 0.079 cfa00500=Starch and sucrose metabolism 16 0.39 52 0.96 0.079 cfa04621=NOD-like receptor signaling pathway 12 0.41 49 0.96 0.080 cfa00410=beta-Alanine metabolism 7 0.47 39 0.97 0.093 cfa00604=Glycosphingolipid biosynthesis - ganglio series 33 0.34 72 0.94 0.094 cfa05146=Amoebiasis 8 0.44 41 0.96 0.097 cfa00900=Terpenoid backbone biosynthesis 4 0.57 15 0.98 0.099 cfa00460=Cyanoamino acid metabolism 4 0.57 15 0.98 0.099 cfa00750=Vitamin B6 metabolism 12 0.40 51 0.95 0.10 cfa00052=Galactose metabolism 12 0.40 51 0.95 0.10 cfa00983=Drug metabolism - other enzymes 9 0.43 46 0.96 0.10 cfa00040=Pentose and glucuronate interconversions 5 0.50 32 0.97 0.11 cfa04122=Sulfur relay system 26 0.35 70 0.93 0.12 cfa04064=NF-kappa B signaling pathway 10 0.40 51 0.94 0.13 cfa05332=Graft-versus-host disease 17 0.36 63 0.92 0.13 cfa00480=Glutathione metabolism 21 0.35 68 0.92 0.13 cfa05133=Pertussis 7 0.44 45 0.95 0.13 cfa00770=Pantothenate and CoA biosynthesis 12 0.38 61 0.92 0.15 cfa03410=Base excision repair 21 0.34 71 0.90 0.15 cfa04976=Bile secretion 15 0.36 65 0.90 0.16 cfa04978=Mineral absorption 4 0.50 32 0.96 0.16 cfa00072=Synthesis and degradation of ketone bodies 50 0.32 78 0.88 0.16 cfa00230=Purine metabolism 8 0.40 51 0.93 0.16 cfa05310=Asthma 6 0.43 46 0.94 0.17 cfa00603=Glycosphingolipid biosynthesis - globo series 2 0.67 8 0.98 0.19 cfa00785=Lipoic acid metabolism 8 0.38 55 0.90 0.20 cfa00062=Fatty acid elongation 8 0.38 55 0.90 0.20 cfa03430=Mismatch repair 11 0.35 67 0.88 0.22 cfa05340=Primary immunodeficiency 12 0.34 73 0.85 0.25 cfa00260=Glycine, serine and threonine metabolism 40 0.31 81 0.81 0.25 cfa04145=Phagosome 42 0.31 82 0.80 0.25 cfa05164=Influenza A 13 0.33 75 0.83 0.27 cfa00970=Aminoacyl-tRNA biosynthesis 1 1.0 1 1.0 0.28 cfa00472=D-Arginine and D-ornithine metabolism 4 0.40 51 0.89 0.29 cfa00130=Ubiquinone and other terpenoid-quinone biosynthesis 4 0.40 51 0.89 0.29 cfa00920=Sulfur metabolism 8 0.35 69 0.84 0.29 cfa00630=Glyoxylate and dicarboxylate metabolism 36 0.30 85 0.76 0.30 cfa04514=Cell adhesion molecules (CAMs) 10 0.33 75 0.81 0.31 cfa00640=Propanoate metabolism 2 0.50 32 0.93 0.31 cfa00730=Thiamine metabolism 7 0.35 68 0.84 0.31 cfa01040=Biosynthesis of unsaturated fatty acids 14 0.32 77 0.78 0.32 cfa05134=Legionellosis 44 0.30 86 0.74 0.32 cfa05168=Herpes simplex infection 11 0.32 76 0.79 0.33 cfa00860=Porphyrin and chlorophyll metabolism 12 0.32 79 0.77 0.36 cfa00620=Pyruvate metabolism 31 0.30 87 0.70 0.38 cfa05145=Toxoplasmosis 6 0.33 75 0.79 0.38 cfa00670=One carbon pool by folate 12 0.31 81 0.73 0.39 cfa04672=Intestinal immune network for IgA production 12 0.31 81 0.73 0.39 cfa04973=Carbohydrate digestion and absorption 14 0.30 84 0.72 0.40 cfa00520=Amino sugar and nucleotide sugar metabolism 11 0.31 83 0.72 0.41 cfa05219=Bladder cancer 23 0.29 88 0.69 0.41 cfa05222=Small cell lung cancer 8 0.31 81 0.72 0.44 cfa00601=Glycosphingolipid biosynthesis - lacto and neolacto series 8 0.31 81 0.72 0.44 cfa04966=Collecting duct acid secretion 5 0.31 80 0.73 0.47 cfa00533=Glycosaminoglycan biosynthesis - keratan sulfate 1 0.50 32 0.92 0.48 cfa00300=Lysine biosynthesis 10 0.29 89 0.67 0.48 cfa03030=DNA replication 12 0.29 90 0.62 0.51 cfa04930=Type II diabetes mellitus 33 0.28 92 0.57 0.51 cfa04110=Cell cycle 16 0.28 91 0.59 0.53 cfa05416=Viral myocarditis 2 0.33 75 0.79 0.53 cfa00400=Phenylalanine, tyrosine and tryptophan biosynthesis 24 0.28 93 0.57 0.53 cfa04972=Pancreatic secretion 5 0.29 89 0.68 0.53 cfa00360=Phenylalanine metabolism 13 0.27 94 0.53 0.59 cfa00310=Lysine degradation 8 0.27 95 0.54 0.62 cfa00250=Alanine, aspartate and glutamate metabolism 8 0.27 95 0.54 0.62 cfa00514=Other types of O-glycan biosynthesis 4 0.27 95 0.59 0.63 cfa00450=Selenocompound metabolism 4 0.27 95 0.59 0.63 cfa01210=2-Oxocarboxylic acid metabolism 11 0.26 97 0.49 0.64 cfa04330=Notch signaling pathway 14 0.26 96 0.49 0.64 cfa00330=Arginine and proline metabolism 4 0.25 100 0.53 0.69 cfa00053=Ascorbate and aldarate metabolism 8 0.25 100 0.45 0.70 cfa00270=Cysteine and methionine metabolism 9 0.25 100 0.44 0.70 cfa04623=Cytosolic DNA-sensing pathway 18 0.25 98 0.39 0.71 cfa04210=Apoptosis 5 0.24 107 0.45 0.73 cfa04140=Regulation of autophagy 14 0.24 104 0.33 0.77 cfa00010=Glycolysis / Gluconeogenesis 7 0.23 111 0.38 0.77 cfa05020=Prion diseases 8 0.24 109 0.37 0.77 cfa00051=Fructose and mannose metabolism 28 0.25 101 0.28 0.79 cfa04380=Osteoclast differentiation 1 0.20 129 0.58 0.80 cfa00524=Butirosin and neomycin biosynthesis 6 0.22 116 0.35 0.80 cfa05216=Thyroid cancer 31 0.25 102 0.25 0.81 cfa05012=Parkinson's disease 15 0.23 110 0.27 0.82 cfa04920=Adipocytokine signaling pathway 16 0.24 109 0.27 0.82 cfa04350=TGF-beta signaling pathway 23 0.24 105 0.24 0.82 cfa05142=Chagas disease (American trypanosomiasis) 9 0.22 114 0.29 0.82 cfa03420=Nucleotide excision repair 17 0.23 112 0.24 0.83 cfa05410=Hypertrophic cardiomyopathy (HCM) 35 0.24 103 0.22 0.83 cfa05202=Transcriptional misregulation in cancer 10 0.22 116 0.26 0.84 cfa05014=Amyotrophic lateral sclerosis (ALS) 13 0.22 115 0.23 0.85 cfa04370=VEGF signaling pathway 26 0.24 108 0.20 0.86 cfa05160=Hepatitis C 31 0.24 106 0.19 0.86 cfa00190=Oxidative phosphorylation 76 0.25 99 0.17 0.86 cfa04151=PI3K-Akt signaling pathway 7 0.21 127 0.24 0.87 cfa04742=Taste transduction 15 0.22 118 0.18 0.88 cfa05218=Melanoma 14 0.22 122 0.17 0.90 cfa05412=Arrhythmogenic right ventricular cardiomyopathy (ARVC) 17 0.22 120 0.15 0.90 cfa05414=Dilated cardiomyopathy 4 0.18 140 0.23 0.90 cfa00534=Glycosaminoglycan biosynthesis - heparan sulfate / heparin 5 0.19 136 0.20 0.90 cfa00030=Pentose phosphate pathway 21 0.22 117 0.13 0.91 cfa04726=Serotonergic synapse 15 0.21 124 0.13 0.92 cfa03008=Ribosome biogenesis in eukaryotes 4 0.17 145 0.19 0.92 cfa04320=Dorso-ventral axis formation 7 0.19 134 0.16 0.92 cfa04960=Aldosterone-regulated sodium reabsorption 22 0.22 121 0.10 0.93 cfa04066=HIF-1 signaling pathway 24 0.22 119 0.11 0.93 cfa04670=Leukocyte transendothelial migration 28 0.22 116 0.10 0.93 cfa05161=Hepatitis B 43 0.23 113 0.095 0.93 cfa04144=Endocytosis 14 0.20 128 0.11 0.94 cfa05220=Chronic myeloid leukemia 5 0.17 146 0.15 0.94 cfa04744=Phototransduction 6 0.18 142 0.13 0.94 cfa04130=SNARE interactions in vesicular transport 12 0.19 133 0.079 0.96 cfa05211=Renal cell carcinoma 23 0.21 125 0.067 0.96 cfa05162=Measles 4 0.15 154 0.11 0.96 cfa03020=RNA polymerase 10 0.18 141 0.063 0.97 cfa00562=Inositol phosphate metabolism 4 0.14 161 0.079 0.97 cfa04710=Circadian rhythm 10 0.17 146 0.047 0.98 cfa05210=Colorectal cancer 15 0.18 139 0.034 0.98 cfa04914=Progesterone-mediated oocyte maturation 20 0.19 133 0.028 0.98 cfa04270=Vascular smooth muscle contraction 40 0.21 123 0.032 0.98 cfa04510=Focal adhesion 8 0.16 150 0.048 0.98 cfa05213=Endometrial cancer 10 0.15 154 0.015 0.99 cfa05212=Pancreatic cancer 10 0.16 149 0.029 0.99 cfa04260=Cardiac muscle contraction 10 0.16 153 0.021 0.99 cfa05214=Glioma 13 0.16 151 0.012 0.99 cfa05215=Prostate cancer 14 0.17 148 0.016 0.99 cfa04012=ErbB signaling pathway 14 0.18 144 0.025 0.99 cfa04620=Toll-like receptor signaling pathway 15 0.17 146 0.017 0.99 cfa04650=Natural killer cell mediated cytotoxicity 17 0.18 143 0.014 0.99 cfa04114=Oocyte meiosis 24 0.18 137 0.010 0.99 cfa04910=Insulin signaling pathway 32 0.20 130 0.015 0.99 cfa05010=Alzheimer's disease 33 0.20 131 0.010 0.99 cfa05016=Huntington's disease 8 0.15 158 0.020 0.99 cfa04730=Long-term depression 9 0.15 157 0.016 0.99 cfa03018=RNA degradation 9 0.15 157 0.016 0.99 cfa04664=Fc epsilon RI signaling pathway 0 0.0 204 0.38 1.0 cfa00471=D-Glutamine and D-glutamate metabolism 1 0.036 201 0.0014 1.0 cfa00020=Citrate cycle (TCA cycle) 1 0.045 198 0.0076 1.0 cfa03060=Protein export 1 0.053 196 0.018 1.0 cfa04964=Proximal tubule bicarbonate reclamation 1 0.059 194 0.030 1.0 cfa00532=Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate 10 0.13 171 0.0017 1.0 cfa04912=GnRH signaling pathway 10 0.13 172 0.0014 1.0 cfa04070=Phosphatidylinositol signaling system 10 0.14 163 0.0053 1.0 cfa05100=Bacterial invasion of epithelial cells 11 0.087 186 1.6E-7 1.0 cfa04310=Wnt signaling pathway 11 0.13 170 0.0012 1.0 cfa04666=Fc gamma R-mediated phagocytosis 11 0.15 156 0.0087 1.0 cfa04970=Salivary secretion 13 0.083 187 1.9E-9 1.0 cfa05034=Alcoholism 13 0.13 167 0.00067 1.0 cfa04660=T cell receptor signaling pathway 15 0.12 173 0.000058 1.0 cfa04360=Axon guidance 15 0.12 173 0.000058 1.0 cfa04530=Tight junction 15 0.12 175 0.000010 1.0 cfa04390=Hippo signaling pathway 15 0.14 164 0.00065 1.0 cfa04722=Neurotrophin signaling pathway 18 0.13 169 0.000042 1.0 cfa03010=Ribosome 18 0.14 165 0.00015 1.0 cfa04120=Ubiquitin mediated proteolysis 18 0.16 152 0.0035 1.0 cfa05322=Systemic lupus erythematosus 2 0.016 203 8.1E-15 1.0 cfa03040=Spliceosome 2 0.028 202 3.3E-8 1.0 cfa03015=mRNA surveillance pathway 26 0.19 135 0.0088 1.0 cfa03013=RNA transport 27 0.15 159 0.000019 1.0 cfa05203=Viral carcinogenesis 28 0.17 145 0.0018 1.0 cfa04141=Protein processing in endoplasmic reticulum 28 0.17 148 0.00087 1.0 cfa04062=Chemokine signaling pathway 29 0.17 147 0.00094 1.0 cfa05169=Epstein-Barr virus infection 3 0.038 200 5.6E-8 1.0 cfa04727=GABAergic synapse 3 0.052 197 0.000014 1.0 cfa04720=Long-term potentiation 3 0.067 189 0.00045 1.0 cfa04961=Endocrine and other factor-regulated calcium reabsorption 3 0.070 188 0.00076 1.0 cfa04962=Vasopressin-regulated water reabsorption 3 0.091 184 0.0090 1.0 cfa05033=Nicotine addiction 30 0.15 155 0.000038 1.0 cfa04810=Regulation of actin cytoskeleton 31 0.18 138 0.0040 1.0 cfa04020=Calcium signaling pathway 34 0.14 160 0.0000011 1.0 cfa04010=MAPK signaling pathway 4 0.061 192 0.000010 1.0 cfa04971=Gastric acid secretion 4 0.098 182 0.0050 1.0 cfa03022=Basal transcription factors 46 0.19 132 0.0017 1.0 cfa05166=HTLV-I infection 5 0.043 199 6.9E-11 1.0 cfa04728=Dopaminergic synapse 5 0.056 195 1.4E-7 1.0 cfa04723=Retrograde endocannabinoid signaling 5 0.062 190 0.0000011 1.0 cfa04540=Gap junction 5 0.11 177 0.0082 1.0 cfa05030=Cocaine addiction 5 0.11 180 0.0066 1.0 cfa03050=Proteasome 5 0.12 175 0.010 1.0 cfa04340=Hedgehog signaling pathway 6 0.059 193 3.4E-8 1.0 cfa04725=Cholinergic synapse 6 0.061 191 7.4E-8 1.0 cfa04724=Glutamatergic synapse 6 0.10 181 0.0012 1.0 cfa05031=Amphetamine addiction 6 0.12 174 0.0084 1.0 cfa05217=Basal cell carcinoma 6 0.12 176 0.0045 1.0 cfa05223=Non-small cell lung cancer 62 0.21 126 0.0038 1.0 cfa05200=Pathways in cancer 66 0.14 162 1.1E-11 1.0 cfa04740=Olfactory transduction 7 0.11 178 0.0016 1.0 cfa04520=Adherens junction 7 0.13 166 0.012 1.0 cfa05221=Acute myeloid leukemia 8 0.090 185 0.000014 1.0 cfa04713=Circadian entrainment 8 0.090 185 0.000014 1.0 cfa04916=Melanogenesis 8 0.095 183 0.000044 1.0 cfa05032=Morphine addiction 8 0.11 179 0.00075 1.0 cfa05132=Salmonella infection 8 0.13 168 0.0068 1.0 cfa04150=mTOR signaling pathway 8 0.13 168 0.0068 1.0 cfa04721=Synaptic vesicle cycle 9 0.14 161 0.0095 1.0 cfa04662=B cell receptor signaling pathway 32 0.68 7 1.0 1.2E-8 cfa03460=Fanconi anemia pathway 34 0.64 9 1.0 4.2E-8 cfa00590=Arachidonic acid metabolism 85 0.45 40 1.0 4.9E-7 cfa04060=Cytokine-cytokine receptor interaction 34 0.60 12 1.0 5.3E-7 cfa04610=Complement and coagulation cascades 408 0.38 60 1.0 8.6E-11 cfa01100=Metabolic pathways
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Douglas R. Cavener Professor and Head Department of Biology 110 Life Science Building Pennsylvania State University University Park, PA 16802
(814) 865-4562 Dept Office (814) 865-9790 Lab Office (814) 865-9131 Fax drc9@psu.edu