Question: Problem With Scientific Notation Sorting And Filtering In Galaxy
0
Douglas Cavener • 10 wrote:
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
--
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
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modified 4.8 years ago
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4.8 years ago by
Douglas Cavener • 10