MetaCyc metagenome - microDM/MicFunPred GitHub Wiki
MetaCyc metagenome
This directory will contain predicted metagenome in terms of EC and MetaCyc pathways.
| File | Description |
|---|---|
| EC_metagenome.tsv.gz | Tab separated, EC metagenome, each column represents samples while rows represents EC |
| RXN_metagenome.tsv.gz | Tab separated, RXN (reactions) metagenome, each column represents samples while rows represents RXN |
| minPath_files | MinPath files |
| PathwayAbundance.tsv.gz | MetaCyc pathway abundance prunned with MinPath |
| PathwayAbundance_with_names.tsv.gz | MetaCyc pathway abundance with names |
| Pathway_summarize_by_Types.tsv.gz | MetaCyc pathway abundance summarized by pathway types |
EC_metagenome.tsv.gz
zcat EC_metagenome.tsv.gz | head
sample1 sample2 sample3
EC:1.- 151.67428571428573 947.9028571428572 0.0
EC:1.1.- 27.94 173.56 0.0
EC:1.1.1.- 68.19428571428571 421.5028571428571 0.0
EC:1.1.1.100 59.55254956383823 330.7300767720253 194.89625
EC:1.1.1.133 25.720000000000002 162.13219780219782 33.98
EC:1.1.1.193 14.31 90.18 116.84
EC:1.1.1.205 25.79201030927835 132.58731958762888 158.26999999999998
EC:1.1.1.22 13.97 128.74 82.86
EC:1.1.1.25 26.958790642347346 140.1390483743061 141.6170833333333
RXN_metagenome.tsv.gz
zcat RXN_metagenome.tsv.gz | head
sample1 sample2 sample3
RXN-9556 59.55254956383823 330.7300767720253 194.89625
RXN-16622 59.55254956383823 330.7300767720253 194.89625
RXN1G-469 59.55254956383823 330.7300767720253 194.89625
RXN1G-349 59.55254956383823 330.7300767720253 194.89625
RXN-9633 59.55254956383823 330.7300767720253 194.89625
RXN-11476 59.55254956383823 330.7300767720253 194.89625
RXN-9518 59.55254956383823 330.7300767720253 194.89625
RXN-16626 59.55254956383823 330.7300767720253 194.89625
RXN-9514 59.55254956383823 330.7300767720253 194.89625
minPath_files
We have focussed more on MetaCyc annotations as compared to KEGG as MetaCyc is freely available for academic users. In this case, we run MinPath individually on each samples and then consolidate the results in PathwayAbundance.tsv.gz
-
sample*_minpath_in.txt
This is just a list of reactions present in corresponding sample
read0 RXN-9556 read1 RXN-16622 read2 RXN1G-469 read3 RXN1G-349 read4 RXN-9633 -
sample*_minpath.out
Typical output of MinPath
path 1 any n/a naive 1 minpath 1 fam0 6 fam-found 5 name PWY-5989 path 2 any n/a naive 1 minpath 0 fam0 6 fam-found 1 name PWY-5972 path 4 any n/a naive 1 minpath 1 fam0 3 fam-found 3 name PWY0-901 path 5 any n/a naive 1 minpath 1 fam0 4 fam-found 2 name PWY-6281 path 6 any n/a naive 1 minpath 1 fam0 25 fam-found 6 name PWY-6944 -
sample*_minpath.out.details
This file lists all pathways found to be activated as per MinPath predictions and also includes reactions found in our data.
path 1 fam0 6 fam-found 5 # PWY-5989 RXN-9633 hits 1 # RXN-9633 RXN-9632 hits 1 # RXN-9632 RXN-9634 hits 1 # RXN-9634 RXN-9635 hits 1 # RXN-9635 RXN-16380 hits 1 # RXN-16380 path 4 fam0 3 fam-found 3 # PWY0-901 2.9.1.1-RXN hits 1 # 2.9.1.1-RXN RXN0-2161 hits 1 # RXN0-2161 2.7.9.3-RXN hits 1 # 2.7.9.3-RXN
PathwayAbundance.tsv.gz
zcat PathwayAbundance.tsv.gz | head
sample1 sample2 sample3
14DICHLORBENZDEG-PWY 15.770257731958763 97.96298969072166 0.0
2PHENDEG-PWY 13.97 86.78 0.0
3-HYDROXYPHENYLACETATE-DEGRADATION-PWY 85.40422680412372 530.521030927835 0.0
ACETOACETATE-DEG-PWY 22.82 1.1423076923076925 0.0
AEROBACTINSYN-PWY 55.88 347.12 0.0
ALACAT2-PWY 28.44407216494845 247.73572429288924 0.0
ALANINE-VALINESYN-PWY 53.78396907216495 307.3871840942562 67.96
ALKANEMONOX-PWY 29.092164948453608 180.71711340206184 0.0
ALL-CHORISMATE-PWY 84.3040206185567 522.3431007137192 0.0
PathwayAbundance_with_names.tsv.gz
zcat PathwayAbundance_with_names.tsv.gz | head
sample1 sample2 sample3 Type Common-Name
14DICHLORBENZDEG-PWY 15.770257731958763 97.96298969072166 0.0 Chlorobenzene-Degradation 1,4-dichlorobenzene degradation
2PHENDEG-PWY 13.97 86.78 0.0 Phenylethylamine-Degradation phenylethylamine degradation I
3-HYDROXYPHENYLACETATE-DEGRADATION-PWY 85.40422680412372 530.521030927835 0.0 AROMATIC-COMPOUNDS-DEGRADATION 4-hydroxyphenylacetate degradation
ACETOACETATE-DEG-PWY 22.82 1.1423076923076925 0.0 Fatty-Acid-and-Lipid-Degradation acetoacetate degradation (to acetyl CoA)
AEROBACTINSYN-PWY 55.88 347.12 0.0 Siderophores-Biosynthesis aerobactin biosynthesis
ALACAT2-PWY 28.44407216494845 247.73572429288924 0.0 ALANINE-DEG L-alanine degradation II (to D-lactate)
ALANINE-VALINESYN-PWY 53.78396907216495 307.3871840942562 67.96
Pathway_summarize_by_Types.tsv.gz
zcat Pathway_summarize_by_Types.tsv.gz | head
Type sample1 sample2 sample3
2-Chloroacrylates-Degradation 0.0 41.96 0.0
3-Chlorocatechol-Degradation 15.770257731958763 97.96298969072166 0.0
3-Dehydroquinate-Biosynthesis 65.26431800158605 326.0534368037461 172.4283333333333
4-Aminobutyraye-Degradation 56.29201030927835 347.56731958762884 0.0
5Z-Dodec-5-enoate-Biosynthesis 171.17986518636005 965.8483995317399 432.11583333333334
6-HM-Dihydropterin-PP-Biosynthesis 28.692010309278352 180.80731958762888 233.68
7-Keto-8-aminopelargonate-Biosynthesis 369.69174068199845 2107.8641186511086 864.2316666666668
ADP-Sugar-Biosynthesis 85.20735395189004 477.8761776367962 372.87
AIR-Biosynthesis 142.8580412371134 797.7955640648012 613.2245833333334
MetaCyc metagenome