KEGG metagenome - microDM/MicFunPred GitHub Wiki
KEGG metagenome
This directory will contain predicted metagenome in terms of KEGG.
| File | Description |
|---|---|
| KO_metagenome.tsv.gz | Tab separated, KO metagenome, each column represents samples while rows represents KO |
| KO_metagenome_with_description.tsv.gz | KO metagenome along with annotations, names and description |
| minpath_in.ko | Input file for running MinPath analysis |
| minpath.out | MinPath output |
| KO_metagenome_minPath_pruned.txt | KO metagenome with prunned KO’s as suggested by MinPath |
| summarized_by_A.tsv.gz | KO metagenome summarized by A level hierarchy |
| summarized_by_B.tsv.gz | KO metagenome summarized by B level hierarchy |
| summarized_by_C.tsv.gz | KO metagenome summarized by C level hierarchy |
| summarized_by_Pathway_Module.tsv.gz | KO metagenome summarized by Pathway Module level hierarchy |
KO_metagenome.tsv.gz
zcat KO_metagenome.tsv.gz | head
sample1 sample2 sample3
K00012 13.97 128.74 82.86
K00014 26.958790642347346 140.1390483743061 141.6170833333333
K00018 0.0 3.4 33.98
K00024 14.042010309278352 87.22731958762887 0.0
K00029 14.042010309278352 87.22731958762887 0.0
K00031 25.596030927835052 90.98195876288659 36.10375
K00054 0.34 0.0 0.0
K00057 30.300384615384615 90.18 116.84
K00058 34.289226804123714 189.0851261659303 141.8025
KO_metagenome_with_description.tsv.gz
zcat KO_metagenome_with_description.tsv.gz | head
sample1 sample2 sample3 A B C EC Pathway_Module
K00001 0.34 2.86 0.0 A09100 Metabolism B 09101 Carbohydrate metabolism C 00010 Glycolysis / Gluconeogenesis [PATH:ko00010] E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
K00001 0.34 2.86 0.0 A09100 Metabolism B 09103 Lipid metabolism C 00071 Fatty acid degradation [PATH:ko00071] E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
K00001 0.34 2.86 0.0 A09100 Metabolism B 09105 Amino acid metabolism C 00350 Tyrosine metabolism [PATH:ko00350] E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
K00001 0.34 2.86 0.0 A09100 Metabolism B 09108 Metabolism of cofactors and vitamins C 00830 Retinol metabolism [PATH:ko00830] E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
K00001 0.34 2.86 0.0 A09100 Metabolism B 09111 Xenobiotics biodegradation and metabolism C 00625 Chloroalkane and chloroalkene degradation [PATH:ko00625] E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
K00001 0.34 2.86 0.0 A09100 Metabolism B 09111 Xenobiotics biodegradation and metabolism C 00626 Naphthalene degradation [PATH:ko00626] E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
K00001 0.34 2.86 0.0 A09100 Metabolism B 09111 Xenobiotics biodegradation and metabolism C 00980 Metabolism of xenobiotics by cytochrome P450 [PATH:ko00980] E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
K00001 0.34 2.86 0.0 A09100 Metabolism B 09111 Xenobiotics biodegradation and metabolism C 00982 Drug metabolism - cytochrome P450 [PATH:ko00982] E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
K00003 11.75 45.36 128.16666666666666 A09100 Metabolism B 09105 Amino acid metabolism C 00260 Glycine, serine and threonine metabolism [PATH:ko00260] hom; homoserine dehydrogenase [EC:1.1.1.3] M00018 Threonine biosynthesis, aspartate => homoserine => threonine [PATH:map00260 map01230 map01100 map01110]
minpath_in.ko
head minpath_in.ko
0 K00001
1 K00001
2 K00001
3 K00001
4 K00001
5 K00001
minpath.out
head minpath.out
path 00010 kegg n/a naive 1 minpath 1 fam0 56 fam-found 38 name Glycolysis / Gluconeogenesis
path 00020 kegg n/a naive 1 minpath 1 fam0 50 fam-found 39 name Citrate cycle (TCA cycle)
path 00030 kegg n/a naive 1 minpath 1 fam0 42 fam-found 27 name Pentose phosphate pathway
path 00031 kegg n/a naive 1 minpath 1 fam0 12 fam-found 7 name Inositol metabolism
path 00040 kegg n/a naive 1 minpath 1 fam0 41 fam-found 26 name Pentose and glucuronate interconversions
path 00051 kegg n/a naive 1 minpath 1 fam0 50 fam-found 28 name Fructose and mannose metabolism
KO_metagenome_minPath_pruned.txt
This file looks like same as KO_metagenome_with_description.tsv.gz. Just we have removed genes belonging to such pathways which are not predicted as active by MinPath.
summarized_by_A.tsv.gz
zcat summarized_by_A.tsv.gz | head
A sample1 sample2 sample3
A09100 Metabolism 32297.33414618055 180852.47009202832 72473.8854166668
A09120 Genetic Information Processing 5293.344144858581 24632.699234205662 19407.103750000017
A09130 Environmental Information Processing 8258.298853819737 46193.38755266034 9134.184583333323
A09140 Cellular Processes 1658.5946841131383 9993.024101280173 639.6029166666667
A09150 Organismal Systems 91.52506740681999 455.39752184585177 94.15291666666666
A09160 Human Diseases 143.79785091197465 785.2144735093086 347.68833333333333
summarized_by_B.tsv.gz
zcat summarized_by_B.tsv.gz | head
B sample1 sample2 sample3
B 09101 Carbohydrate metabolism 10684.74487681733 62933.709609908896 17771.494583333337
B 09102 Energy metabolism 3956.882752048634 21252.286031456515 7944.377916666657
B 09103 Lipid metabolism 1913.8600383293674 10167.229569162802 3867.653333333334
B 09104 Nucleotide metabolism 2613.2188651863585 13652.647095502443 6731.11
B 09105 Amino acid metabolism 4930.433769495102 27830.393154714722 12383.185833333338
B 09106 Metabolism of other amino acids 1439.8528691514664 8013.301064574602 2728.412916666667
B 09107 Glycan biosynthesis and metabolism 1110.2449894263818 6676.253522034667 4709.720833333333
B 09108 Metabolism of cofactors and vitamins 4076.5835352894487 21580.36699324047 12432.723333333339
B 09109 Metabolism of terpenoids and polyketides 713.9688567274651 3691.015540236398 2316.9445833333334
summarized_by_C.tsv.gz
zcat summarized_by_C.tsv.gz | head
C sample1 sample2 sample3
C 00010 Glycolysis / Gluconeogenesis [PATH:ko00010] 1102.994571768438 7198.3517394735845 2258.4908333333333
C 00020 Citrate cycle (TCA cycle) [PATH:ko00020] 546.1885091197463 3139.4692442505943 1095.4508333333333
C 00030 Pentose phosphate pathway [PATH:ko00030] 838.3170644990751 4057.839739398059 1528.1229166666665
C 00040 Pentose and glucuronate interconversions [PATH:ko00040] 494.5774451493525 2622.8329608020854 371.0495833333333
C 00051 Fructose and mannose metabolism [PATH:ko00051] 728.2310983346551 4136.708726029984 963.0029166666667
C 00052 Galactose metabolism [PATH:ko00052] 636.6226777689666 3366.691655526605 1065.9541666666667
C 00053 Ascorbate and aldarate metabolism [PATH:ko00053] 257.3911895321174 1558.8207216494845 165.72
C 00061 Fatty acid biosynthesis [PATH:ko00061] 477.70229579698645 2651.3178949813073 1353.3179166666669
C 00071 Fatty acid degradation [PATH:ko00071] 400.8355736188212 2140.8091411578116 502.08166666666665