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Merge pull request #28 from trjhensen/master
Script deposit for paper titled: "In silico metabolic modelling links microbiome-derived metabolites to risk factors of Alzheimer’s disease"
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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/.Rhistory

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/AlzheimerRiskFactorAnalysisMetabolism.Rproj

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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX

‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/AnalysisPipeline.Rmd

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/AnalysisPipeline.nb.html

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/Figures/Fig_1.png

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/Figures/Fig_1.svg

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/Figures/Fig_2.png

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/Figures/Fig_2.svg

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/Figures/Fig_3.png

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/Figures/Fig_3.svg

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/Figures/Fig_4.png

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/Figures/Fig_4.svg

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/README.txt

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Please make sure that the following files are present in the "inputs" folder:
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1. flux_results.xlsx
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2. Bile_acids_Corrected_table.xlsx
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3. MARS_species.csv
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4. KNN_imputed_metabolon_data_3rdMarch.xlsx
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5. metadata.csv
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6. microbiome_abundances_and_taxonomy.csv
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7. microbiome_annotations.csv
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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/inputs/gf_fluxes.csv

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sex,12dhchol,2hb,2mbut,3aib,3dhcdchol,3dhchol,3dhdchol,3dhlchol,4aabutn,4abut,7dhcdchol,7klitchol,7ocholate,C02356,C02528,CE1273,CE1292,CE2345,CE3038,HC02191,HC02192,HC02193,HC02194,HC02195,HC02196,HC02197,HC02198,L2aadp,Lkynr,M01989,ac,ach,ala_L,amet,arg_L,asn_L,asp_L,but,ca24g,ca3s,cdca24g,cdca3g,chol,cholate,chsterol,chsterols,coprost,creat,cspg_d,cys_L,dca24g,dca3g,dca3s,dchac,ddeccrn,dgchol,dhcholestanate,dopa,dopasf,duri,fald,for,g3pc,gca3s,gcdca3s,gchola,gdca3s,glc_D,gln_L,glu_L,gly,glyb,gthox,gudca3s,hca24g,hca6g,hdca24g,hdca6g,his_L,hista,hyochol,hyptaur,icdchol,ile_L,ind3ac,indole,inds,isobut,isochol,isoval,lac_L,lca24g,lca3g,lca3s,leu_L,lineth,lys_L,met_L,mlthf,nrpphr,nrpphrsf,orn,pchol_hs,pcs,phe_L,ppa,pro_L,ptrc,sarcs,ser_L,sphmyln_hs,sprm,srtn,taur,tca3s,tcdca3s,tchola,tdca3s,tdchola,tdechola,thcholstoic,thr_L,thyochol,trp_L,tudca3s,tyr_L,uchol,udca3s,udpglcur,urate,uri,val_L,xmp,xol24oh,xol25oh,xol27oh,xol7ah3,xol7aone,xoldiolone,xoltri24,xoltri25,xoltri27,xtsn
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1,0,10066.65527,0,1699.277895,0,0,0,-3.31E-12,1699.284421,1699.275874,0,0.3010176,0,98.77670906,24.19085852,0,0.01008,0.01008,0.01008,0,0,0,0,24.19085852,24.19085852,0,0,40.23572438,5.452024899,0,24988.31586,1608.320352,1699.275874,56.72960705,461.8442706,849.6379369,1699.275874,31.60110773,24.98931373,24.98931373,24.19085852,24.19085852,1577.592445,24.98931373,1234.305876,186.1260362,0,615.7923607,37.22520725,136.1260362,24.98931373,24.98931373,0,0,50,24.19085852,658.5417405,43.20058799,43.20058799,849.6379369,5338.627746,4386.653212,1358.222937,24.98931373,24.19085855,24.98931373,24.98931373,7512.902643,849.6379369,1699.275874,1699.275874,1555.684531,68.06301812,24.19085852,24.19085852,24.19085852,-1.88E-13,0,66.69808614,116.6980861,24.19085852,214.7857112,0,34.51004693,5.452024899,0,0,0,0,0,16658.87724,0,0,0,55.70105702,0.00424336,39.36136717,56.72960705,69.99953975,43.20058799,43.20058799,849.6379369,112.9736354,0,24.58952987,15143.45796,1699.275874,849.6379369,1699.283321,1699.275874,120.0668328,19.99751619,5.452022306,214.7857112,24.98931373,24.19085852,24.98931373,24.98931373,24.19085852,24.98931373,587.1325982,30.73378787,24.19085852,5.452022306,24.19085852,43.20058799,0,24.19085852,800.213647,430.2634712,849.6379369,44.97645617,430.2364467,2.385502133,805.9071892,10.43766209,668.3263158,1217.824029,4.10310144,1220.910043,0.01008,1201.425634,430.2364467
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0,0,4732.08253,0,1642.404,0,0,0,-2.47E-12,1642.401142,1642.399134,0,0.316510535,0,87.54352321,24.22279673,0,0.01008,0.01008,0.01008,0,0,0,0,24.22279673,24.22279673,0,0,39.43253494,5.453624241,0,10258.40208,1456.318646,1642.399134,278.1896039,447.6466724,821.1995668,1642.399134,31.60110773,25.18094298,25.18094298,24.22279673,24.22279673,1486.372752,25.18094298,553.4662929,2.555725593,0,596.8622298,37.39966102,136.9983051,25.18094298,25.18094298,0,0,50,24.22279673,488.4694774,43.25096891,43.25096891,821.1995668,4684.53916,4409.954704,1186.423812,25.18094298,24.22279673,25.18094298,25.18094298,2761.553921,821.1995668,1642.399134,1642.399134,1488.543453,68.49915256,24.22279673,24.22279673,24.22279673,0,0,66.71328229,116.7132823,24.22279673,215.65798,0,34.54443389,5.453624241,0,0,0,0,0,6617.040013,0,0,1.32E-12,55.76662728,0.00424336,39.43253494,531.0876809,69.99961186,43.25096891,43.25096891,821.1995668,116.6365658,0,24.62071944,5804.573966,1642.399134,821.1995668,1642.407476,1642.399134,190.4883043,20.10155665,5.453624241,215.65798,25.18094298,24.22279673,25.18094298,25.18094298,24.22279673,25.18094298,463.2555867,30.77137229,24.22279673,5.453624241,24.22279673,43.25096891,0,24.22279673,757.8930793,416.0647678,821.1995668,45.01884042,416.0319626,11.35483004,475.1291264,481.3505767,550.406576,553.6771463,8.847578212,551.5011893,0.01008,536.1751879,416.0319626

‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/inputs/metaboliteList.xlsx

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/inputs/metaboliteMicrobeLinks.xlsx

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/inputs/microbiome_annotations.csv

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‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/overleaf/ageCognitionMicrobeResults.txt

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metabolite,term,p.value,FDR
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Parabacteroides distasonis,AgeERGO5,0.0928387044846326,0.559269216173587
3+
Collinsella aerofaciens,AgeERGO5,0.115431187600583,0.559269216173587
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Bilophila wadsworthia,AgeERGO5,0.150741249558212,0.559269216173587
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Butyrivibrio crossotus,AgeERGO5,0.195479177190023,0.607014287063756
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Eggerthella lenta,AgeERGO5,0.778952893384131,0.991877224219603
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Butyrivibrio crossotus,Flux,0.0119412672029728,0.352267382487698
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Eggerthella lenta,Flux,0.37667064181971,0.796145516654943
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Parabacteroides distasonis,Flux,0.6705617081665,0.879180906262744
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Collinsella aerofaciens,Flux,0.862489210996214,0.936036042582067
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Bilophila wadsworthia,Flux,0.977674929083779,0.977674929083779

‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/overleaf/ageCognitionfluxresults.txt

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metabolite,term,p.value,FDR
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L-arginine,AgeERGO5,1.13271158211844e-07,4.64411748668559e-06
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3-dehydro-CA/CDCA,AgeERGO5,0.0248725926088912,0.50988814848227
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7-dehydro-CA/CDCA,AgeERGO5,0.212016368923768,0.624179081909905
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Lithocholate,AgeERGO5,0.948051987130371,0.996533606840899
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Deoxycholate,AgeERGO5,0.995095643117638,0.996533606840899
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Deoxycholate,Flux,0.00121153297112155,0.0298369012058947
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Lithocholate,Flux,0.0014554585954095,0.0298369012058947
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7-dehydro-CA/CDCA,Flux,0.00716963009627344,0.0979849446490704
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3-dehydro-CA/CDCA,Flux,0.288459073477148,0.97276375025947
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L-arginine,Flux,0.77353683719554,0.97276375025947

‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/overleaf/apoePvalues.txt

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metabolite,kruskall_p,E2_E3,E2_E4,E3_E4
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Deoxycholate,0.0176,0.00917529705445059,0.00709498983203948,0.723034386243759
3+
S-Adenosyl-L-methionine,0.0325,0.065583213938996,0.867664778401088,0.0264299811328079
4+
7-dehydro-CA/CDCA,0.0739,0.0711449021458291,0.651808593089235,0.0767812508937403
5+
Formaldehyde,0.076,0.0663459640953498,0.609599578761446,0.08784028991989
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Formate,0.099,0.0455829610194464,0.322431743407562,0.224802701374279
7+
Bacteroides thetaiotaomicron,0.0415,0.0121158020865143,0.0913305795309681,0.40562032542807
8+
Eggerthella lenta,0.125,0.103235142396518,0.0422839794298149,0.469781771485342
9+
Butyricimonas virosa,0.198,0.139398980099526,0.0820854396072031,0.579072991014632
10+
Bacteroides caccae,0.21,0.359180799072961,0.0917666339676261,0.201101181172825
11+
Bacteroides finegoldii,0.259,0.100190886262861,0.21159888001184,0.738550926109685
12+
Parabacteroides distasonis,0.328,0.178075814530166,0.148579632568171,0.741389706785968
13+
Dorea formicigenerans,0.347,0.760734791867257,0.238724432407661,0.18721676112057
14+
Faecalibacterium prausnitzii,0.361,0.748064102219309,0.500513535565728,0.153309399802483
15+
Blautia massiliensis,0.376,0.62269273771612,0.215334692993213,0.243817509704037
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Bacteroides ovatus,0.528,0.263666582634726,0.33698487581342,0.919052706157562
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Bifidobacterium longum,0.537,0.88475756825196,0.393969438431207,0.297433847605329
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Bilophila wadsworthia,0.591,0.560105909836181,0.31443329859907,0.506538281072441
19+
Blautia faecis,0.649,0.754525341870954,0.415992804547968,0.432307743316756
20+
Phascolarctobacterium faecium,0.674,0.955446422171568,0.557494036410382,0.392390279275044
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Bacteroides fragilis,0.751,0.692923306316759,0.478856273636146,0.578378163960831
22+
Bacteroides stercoris,0.818,0.5257774064215,0.645264334071502,0.865050355649843
23+
Parabacteroides merdae,0.827,0.734510239249612,0.936346667429157,0.564109417537229
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Bacteroides vulgatus,0.834,0.84520058781072,0.81203431420917,0.548930195054266
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Roseburia inulinivorans,0.967,0.933014834331878,0.823309873802746,0.826071044636631
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Fusicatenibacter saccharivorans,0.972,0.996448665270805,0.871330603084477,0.816334237605896
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cholesterol,0.00608,0.0331981610817383,0.00167898642448631,0.0587620644813704
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deoxycholate,0.0131,0.00408313058963144,0.00755045190608922,0.961846276377847
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4-cholesten-3-one,0.0304,0.538254636542214,0.0393713993943099,0.0169627150323551
30+
7-alpha-hydroxy-3-oxo-4-cholestenoate (7-Hoca),0.0588,0.800008315665333,0.211630071116626,0.0178682179581504
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glycolithocholate,0.0871,0.279752680129129,0.0419092380917279,0.0965000760032608
32+
ursodeoxycholate,0.226,0.116077909389401,0.0934717242212669,0.711075101617172
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taurochenodeoxycholate,0.26,0.899376947620817,0.270200876987765,0.115025315839296
34+
3b-hydroxy-5-cholenoic acid,0.268,0.147959715637536,0.11078601909656,0.673362231209422
35+
glycohyocholate,0.29,0.714582865220178,0.220373589107968,0.155388161083569
36+
taurocholate,0.296,0.606599365052362,0.620345631496737,0.121513893814228
37+
glycochenodeoxycholate,0.301,0.629297646079687,0.199196546382318,0.17961628717964
38+
isoursodeoxycholate,0.306,0.140987671066489,0.150198903152959,0.892407408413057
39+
glycocholate,0.372,0.903347009122621,0.445925854545259,0.162572204023731
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taurodeoxycholate,0.389,0.763471228529454,0.560078493833639,0.169602971825544
41+
hyocholate,0.446,0.273540169004237,0.20725871417075,0.684935882103781
42+
glycochenodeoxycholate glucuronide (1),0.453,0.316100525711953,0.744203665637315,0.340998389625355
43+
glycoursodeoxycholate,0.485,0.372226927780133,0.230139113362541,0.544582216405226
44+
taurocholenate sulfate*,0.603,0.325218265575356,0.515893961750005,0.683326977855205
45+
glycoursodeoxycholic acid sulfate (1),0.62,0.8176203356669,0.689447228691198,0.328317790880508
46+
taurochenodeoxycholic acid 3-sulfate,0.635,0.7029234606027,0.815834634332601,0.350947685357524
47+
cholesterol sulfate,0.636,0.345622588598082,0.409740418002442,0.944958962486269
48+
glycochenodeoxycholate 3-sulfate,0.698,0.815484019725366,0.494032306001194,0.453362160186747
49+
glycodeoxycholate 3-sulfate,0.725,0.800702670779619,0.790207176153247,0.425931500198656
50+
glyco-beta-muricholate**,0.727,0.612094202758972,0.981360748977837,0.478923009968408
51+
taurodeoxycholic acid 3-sulfate,0.732,0.652569216563694,0.451601366798306,0.588446740577174
52+
glycocholenate sulfate*,0.739,0.510141407035984,0.439122458608512,0.788568630973263
53+
taurolithocholate 3-sulfate,0.755,0.453911420407824,0.555876749721902,0.873128318803094
54+
glycolithocholate sulfate*,0.787,0.488860313877258,0.591345398061057,0.873315015721604
55+
deoxycholic acid glucuronide,0.84,0.593633842523626,0.564051077711701,0.890691223452622
56+
lithocholate sulfate (1),0.852,0.876018000008103,0.647723625960665,0.616511459418886

‎Scripts_AD_microbiome_WBM_Hensen_et_al_2024/overleaf/cognitionSerumResults.txt

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metabolite,estimate,pvalue,FDR
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glycochenodeoxycholate glucuronide (1),-0.134722578911793,0.0109128787239837,0.381950755339428
3+
glycochenodeoxycholate 3-sulfate,-0.100657671877885,0.0456959760755559,0.442871617168285
4+
taurodeoxycholic acid 3-sulfate,-0.0884954058764179,0.071381572565526,0.442871617168285
5+
taurochenodeoxycholic acid 3-sulfate,-0.083841444702603,0.0885743234336571,0.442871617168285
6+
glycocholate,-0.0784290461005143,0.115480098800978,0.465181738914604
7+
glycochenodeoxycholate,-0.0657824380822613,0.183912616835151,0.549723965260789
8+
taurochenodeoxycholate,-0.0641436477247419,0.191748684596945,0.549723965260789
9+
glycodeoxycholate 3-sulfate,-0.0634869740897948,0.200004468469881,0.549723965260789
10+
taurocholate,-0.0563694899428194,0.25571803205497,0.58354060956889
11+
isoursodeoxycholate,-0.0553695335711294,0.262200010324548,0.58354060956889
12+
glycohyocholate,-0.0553945830087142,0.266761421517207,0.58354060956889
13+
glyco-beta-muricholate**,-0.0515913355484116,0.29388801497998,0.6050635602529
14+
glycoursodeoxycholic acid sulfate (1),-0.0496796664776591,0.330052838984365,0.610416946705525
15+
taurolithocholate 3-sulfate,-0.0438174386187495,0.372118874511834,0.610416946705525
16+
deoxycholic acid glucuronide,0.0443433385080555,0.383690652214901,0.610416946705525
17+
lithocholate sulfate (1),-0.0357468308067499,0.472047780989708,0.683014748181352
18+
ursodeoxycholate,-0.0338980462971101,0.495221988180848,0.683014748181352
19+
taurodeoxycholate,-0.0327326597973049,0.50738238436329,0.683014748181352
20+
glycoursodeoxycholate,-0.0257870427257578,0.602235258293915,0.752794072867393
21+
glycolithocholate,-0.0204993137414074,0.677719777512618,0.817937662515229
22+
deoxycholate,0.0186129141980269,0.712012446874131,0.818426267810331
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hyocholate,0.0131215449195742,0.793280770082763,0.867650842278022
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glycolithocholate sulfate*,-0.00977785621039839,0.842701505409096,0.893774323918738

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