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chore: new version
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haowang-bioinfo committed Jun 21, 2022
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -13,13 +13,13 @@ This repository contains the latest version of Human-GEM, a human genome-scale m

If you use Human1 in your research, please cite:

> J. L. Robinson, P. Kocabaş, H. Wang, P.-E. Cholley, et al. An atlas of human metabolism. _Sci. Signal._ 13, eaaz1482 (2020). [doi:10.1126/scisignal.aaz1482](https://doi.org/10.1126/scisignal.aaz1482)
> J. L. Robinson, P. Kocabas�, H. Wang, P.-E. Cholley, et al. An atlas of human metabolism. _Sci. Signal._ 13, eaaz1482 (2020). [doi:10.1126/scisignal.aaz1482](https://doi.org/10.1126/scisignal.aaz1482)
Starting from Human-GEM v1.5.0, all the releases are also archived in [Zenodo](https://doi.org/10.5281/zenodo.4099692) from which specific version can be cited if used.

If you use Mouse1, Rat1, Zebrafish1, Fruitfly1, or Worm1 in your research, please cite:

> H. Wang, J. L. Robinson, P. Kocabaş, J. Gustafsson, M. Anton, P.-E. Cholley, et al. Genome-scale metabolic network reconstruction of model animals as a platform for translational research. _PNAS_ 118, e2102344118 (2021). [doi.org/10.1073/pnas.2102344118](https://doi.org/10.1073/pnas.2102344118)
> H. Wang, J. L. Robinson, P. Kocabas�, J. Gustafsson, M. Anton, P.-E. Cholley, et al. Genome-scale metabolic network reconstruction of model animals as a platform for translational research. _PNAS_ 118, e2102344118 (2021). [doi.org/10.1073/pnas.2102344118](https://doi.org/10.1073/pnas.2102344118)


Expand All @@ -39,7 +39,7 @@ If you use Mouse1, Rat1, Zebrafish1, Fruitfly1, or Worm1 in your research, pleas

|Taxonomy | Template Model | Reactions | Metabolites| Genes |
| ------------- |:-------------:|:-------------:|:-------------:|:-----:|
|_Homo sapiens_ | HMR2, Recon3D, iHsa| 13069| 8366| 3067|
|_Homo sapiens_ | HMR2, Recon3D, iHsa| 13070| 8369| 3067|


## Contributing
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15 changes: 8 additions & 7 deletions model/Human-GEM.txt
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Expand Up @@ -411,10 +411,10 @@ MAR04806 MAM00266c + MAM01940c -> MAM02039c + MAM02575c + MAM02980c ENSG000001
MAR05394 MAM02038c + MAM02040c -> MAM02578c + MAM03149c 0.00 1000.00 0.00
MAR06625 MAM01371m + MAM01673m -> MAM01285m + MAM01755m + MAM02039m ENSG00000166548 0.00 1000.00 0.00
MAR06626 MAM01755m + MAM02040m -> MAM01673m + MAM02751m ENSG00000125458 or ENSG00000205309 0.00 1000.00 0.00
MAR07160 0.3 MAM01642c + 0.2 MAM01645c + 0.2 MAM01688c + 0.3 MAM01753c -> MAM01721c + MAM02759c ( ENSG00000115350 and ENSG00000148229 ) or ( ENSG00000062822 and ENSG00000077514 and ENSG00000106628 and ENSG00000175482 ) or ( ENSG00000014138 and ENSG00000101868 ) or ( ENSG00000014138 and ENSG00000062822 and ENSG00000077514 and ENSG00000100479 and ENSG00000101868 and ENSG00000106628 and ENSG00000115350 and ENSG00000148229 and ENSG00000175482 and ENSG00000177084 ) or ENSG00000009413 or ENSG00000051341 or ENSG00000070501 or ENSG00000101751 or ENSG00000111445 or ENSG00000112941 or ENSG00000122008 or ENSG00000122678 or ENSG00000130997 or ENSG00000132382 or ENSG00000140521 or ENSG00000166169 or ENSG00000170734 or ENSG00000256525 0.00 1000.00 0.00
MAR07161 0.18 MAM01371c + 0.3 MAM01623c + 0.34 MAM02034c + 0.18 MAM03130c -> MAM02759c + MAM02847c ( ENSG00000113356 or ENSG00000121851 ) and ( ENSG00000090060 or ENSG00000115421 or ENSG00000164329 or ENSG00000218823 ) and ( ENSG00000083223 or ENSG00000134744 or ENSG00000149016 ) and ENSG00000005075 and ENSG00000013503 and ENSG00000047315 and ENSG00000058600 and ENSG00000066379 and ENSG00000068654 and ENSG00000099817 and ENSG00000099821 and ENSG00000100142 and ENSG00000100413 and ENSG00000102978 and ENSG00000105258 and ENSG00000107951 and ENSG00000125630 and ENSG00000132664 and ENSG00000137054 and ENSG00000144231 and ENSG00000147669 and ENSG00000148606 and ENSG00000161980 and ENSG00000163882 and ENSG00000168002 and ENSG00000168495 and ENSG00000171453 and ENSG00000177700 and ENSG00000181222 and ENSG00000186141 and ENSG00000186184 0.00 1000.00 0.00
MAR07162 0.18 MAM01285c + 0.3 MAM01424c + 0.34 MAM01948c + 0.18 MAM03106c -> MAM02751c + MAM02847c ( ENSG00000113356 or ENSG00000121851 ) and ( ENSG00000090060 or ENSG00000115421 or ENSG00000164329 or ENSG00000218823 ) and ( ENSG00000083223 or ENSG00000134744 or ENSG00000149016 ) and ENSG00000005075 and ENSG00000013503 and ENSG00000047315 and ENSG00000058600 and ENSG00000066379 and ENSG00000068654 and ENSG00000099817 and ENSG00000099821 and ENSG00000100142 and ENSG00000100413 and ENSG00000102978 and ENSG00000105258 and ENSG00000107951 and ENSG00000125630 and ENSG00000132664 and ENSG00000137054 and ENSG00000144231 and ENSG00000147669 and ENSG00000148606 and ENSG00000161980 and ENSG00000163882 and ENSG00000168002 and ENSG00000168495 and ENSG00000171453 and ENSG00000177700 and ENSG00000181222 and ENSG00000186141 and ENSG00000186184 0.00 1000.00 0.00
MAR07163 MAM01721c + MAM02040c -> 0.3 MAM01639c + 0.2 MAM01644c + 0.2 MAM01686c + 0.3 MAM01752c + MAM02039c ( ENSG00000113456 and ENSG00000172613 ) or ENSG00000164053 or ENSG00000183479 or ENSG00000213689 0.00 1000.00 0.00
MAR07160 0.3 MAM01642n + 0.2 MAM01645n + 0.2 MAM01688n + 0.3 MAM01753n -> MAM01721n + MAM02759n ( ENSG00000115350 and ENSG00000148229 ) or ( ENSG00000062822 and ENSG00000077514 and ENSG00000106628 and ENSG00000175482 ) or ( ENSG00000014138 and ENSG00000101868 ) or ( ENSG00000014138 and ENSG00000062822 and ENSG00000077514 and ENSG00000100479 and ENSG00000101868 and ENSG00000106628 and ENSG00000115350 and ENSG00000148229 and ENSG00000175482 and ENSG00000177084 ) or ENSG00000009413 or ENSG00000051341 or ENSG00000070501 or ENSG00000101751 or ENSG00000111445 or ENSG00000112941 or ENSG00000122008 or ENSG00000122678 or ENSG00000130997 or ENSG00000132382 or ENSG00000140521 or ENSG00000166169 or ENSG00000170734 or ENSG00000256525 0.00 1000.00 0.00
MAR07161 0.18 MAM01371n + 0.3 MAM01623n + 0.34 MAM02034n + 0.18 MAM03130n -> MAM02759n + MAM02847n ( ENSG00000113356 or ENSG00000121851 ) and ( ENSG00000090060 or ENSG00000115421 or ENSG00000164329 or ENSG00000218823 ) and ( ENSG00000083223 or ENSG00000134744 or ENSG00000149016 ) and ENSG00000005075 and ENSG00000013503 and ENSG00000047315 and ENSG00000058600 and ENSG00000066379 and ENSG00000068654 and ENSG00000099817 and ENSG00000099821 and ENSG00000100142 and ENSG00000100413 and ENSG00000102978 and ENSG00000105258 and ENSG00000107951 and ENSG00000125630 and ENSG00000132664 and ENSG00000137054 and ENSG00000144231 and ENSG00000147669 and ENSG00000148606 and ENSG00000161980 and ENSG00000163882 and ENSG00000168002 and ENSG00000168495 and ENSG00000171453 and ENSG00000177700 and ENSG00000181222 and ENSG00000186141 and ENSG00000186184 0.00 1000.00 0.00
MAR07162 MAM02751c + MAM02847c -> 0.18 MAM01285c + 0.3 MAM01424c + 0.34 MAM01948c + 0.18 MAM03106c ( ENSG00000113356 or ENSG00000121851 ) and ( ENSG00000090060 or ENSG00000115421 or ENSG00000164329 or ENSG00000218823 ) and ( ENSG00000083223 or ENSG00000134744 or ENSG00000149016 ) and ENSG00000005075 and ENSG00000013503 and ENSG00000047315 and ENSG00000058600 and ENSG00000066379 and ENSG00000068654 and ENSG00000099817 and ENSG00000099821 and ENSG00000100142 and ENSG00000100413 and ENSG00000102978 and ENSG00000105258 and ENSG00000107951 and ENSG00000125630 and ENSG00000132664 and ENSG00000137054 and ENSG00000144231 and ENSG00000147669 and ENSG00000148606 and ENSG00000161980 and ENSG00000163882 and ENSG00000168002 and ENSG00000168495 and ENSG00000171453 and ENSG00000177700 and ENSG00000181222 and ENSG00000186141 and ENSG00000186184 0.00 1000.00 0.00
MAR07163 MAM01721n + MAM02040n -> 0.3 MAM01639n + 0.2 MAM01644n + 0.2 MAM01686n + 0.3 MAM01752n + MAM02039n ( ENSG00000113456 and ENSG00000172613 ) or ENSG00000164053 or ENSG00000183479 or ENSG00000213689 0.00 1000.00 0.00
MAR07164 MAM02040c + MAM02847c -> 0.18 MAM01334c + 0.3 MAM01590c + 0.34 MAM02016c + MAM02039c + 0.18 MAM03114c ( ENSG00000113456 and ENSG00000172613 ) or ENSG00000164053 or ENSG00000183479 or ENSG00000213689 0.00 1000.00 0.00
MAR07713 MAM01334l + MAM02040l -> MAM01280l + MAM02751l ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309 or ENSG00000250741 0.00 1000.00 0.00
MAR07716 MAM02040l + MAM03114l -> MAM02751l + MAM03123l ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309 or ENSG00000250741 0.00 1000.00 0.00
Expand Down Expand Up @@ -1326,7 +1326,7 @@ MAR04084 MAM02040c + MAM02681c -> MAM01334c + MAM02751c ENSG00000104331 or ENS
MAR04187 MAM02040c + MAM02682c -> MAM01283c + MAM02751c ENSG00000104331 or ENSG00000162813 0.00 1000.00 0.00
MAR04188 2 MAM02039c + 4 MAM02555c + MAM02682c -> MAM01267c + 3 MAM02040c + 4 MAM02554c + MAM02681c 0.00 1000.00 0.00
MAR04701 MAM01708c + MAM02039c + MAM02871c -> MAM02877c + MAM02880c ENSG00000123453 or ENSG00000132837 0.00 1000.00 0.00
MAR04840 MAM02040c + MAM02043c -> 2 MAM02039c + MAM02042c + MAM02946c ENSG00000198610 0.00 1000.00 0.00
MAR04840 MAM02040c + MAM02043c -> 2 MAM02039c + MAM02042c + MAM02946c 0.00 1000.00 0.00
MAR04842 MAM02877c -> MAM01266c + MAM02871c ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254 0.00 1000.00 0.00
MAR08662 MAM01597m + MAM02034m + MAM02191m <=> MAM01948m + MAM02192m + MAM02751m ( ENSG00000163541 and ENSG00000172340 ) or ( ENSG00000136143 and ENSG00000163541 ) -1000.00 1000.00 0.00
MAR08663 MAM01285m + MAM02192m + MAM02751m <=> MAM01371m + MAM01597m + MAM02191m ( ENSG00000163541 and ENSG00000172340 ) or ( ENSG00000136143 and ENSG00000163541 ) -1000.00 1000.00 0.00
Expand Down Expand Up @@ -7191,7 +7191,6 @@ MAR08363 MAM01260c <=> MAM01260n -1000.00 1000.00 0.00
MAR08412 MAM02631c <=> MAM02631n -1000.00 1000.00 0.00
MAR08447 MAM01630c <=> MAM01630n -1000.00 1000.00 0.00
MAR08476 MAM01668c <=> MAM01668n ENSG00000112759 or ENSG00000174669 -1000.00 1000.00 0.00
MAR08639 MAM01721c <=> MAM01721n ENSG00000030066 and ENSG00000047410 and ENSG00000058804 and ENSG00000069248 and ENSG00000075188 and ENSG00000085415 and ENSG00000093000 and ENSG00000094914 and ENSG00000095319 and ENSG00000101146 and ENSG00000102900 and ENSG00000108559 and ENSG00000110713 and ENSG00000111581 and ENSG00000113569 and ENSG00000119392 and ENSG00000120253 and ENSG00000124789 and ENSG00000125450 and ENSG00000126883 and ENSG00000132182 and ENSG00000136243 and ENSG00000138750 and ENSG00000139496 and ENSG00000153201 and ENSG00000153207 and ENSG00000155561 and ENSG00000157020 and ENSG00000157349 and ENSG00000163002 and ENSG00000196313 and ENSG00000213024 -1000.00 1000.00 0.00
MAR08789 MAM02581c <=> MAM02581n -1000.00 1000.00 0.00
MAR08828 MAM02750c <=> MAM02750n -1000.00 1000.00 0.00
MAR08837 MAM02736c <=> MAM02736n -1000.00 1000.00 0.00
Expand Down Expand Up @@ -9741,7 +9740,6 @@ MAR08969 MAM02040e + MAM01828e -> MAM02751e + MAM02842e ENSG00000143727 or ENS
MAR08970 MAM01806c <=> MAM01806r -1000.00 1000.00 0.00
MAR08971 3 MAM01968c + 3 MAM02554c -> 3 MAM01961c + 3 MAM02039c + 3 MAM02555c ENSG00000160211 0.00 1000.00 0.00
MAR08972 MAM01974e + MAM02519e + MAM02770c -> MAM01974c + MAM02519c + MAM02770e ENSG00000115902 0.00 1000.00 0.00
MAR08973 3 MAM01169c + 3 MAM02554c -> 3 MAM01596c + 3 MAM02555c + 3 MAM02846c ENSG00000142657 0.00 1000.00 0.00
MAR08974 MAM02630e + 2 MAM02157e -> 2 MAM02961e 0.00 1000.00 0.00
MAR08975 MAM01371c + MAM02170c -> MAM01285c + MAM02039c + MAM02167c 0.00 1000.00 0.00
MAR08976 MAM02039c + MAM02200e <=> MAM02039e + MAM02200c -1000.00 1000.00 0.00
Expand Down Expand Up @@ -13068,3 +13066,6 @@ MAR10130 MAM02961c + MAM10042c -> MAM01597c + MAM02966c 0.00 1000.00 0.00
MAR10131 MAM01986c + MAM10042c -> MAM01597c + MAM02004c 0.00 1000.00 0.00
MAR10132 MAM10041e <=> -1000.00 1000.00 0.00
MAR13083 MAM02039c + MAM02157c + MAM02553c + MAM02630c -> MAM02040c + MAM02552c + MAM02961c ENSG00000010932 0.00 1000.00 0.00
MAR13084 MAM01639c <=> MAM01639n -1000.00 1000.00 0.00
MAR13085 MAM01686c <=> MAM01686n -1000.00 1000.00 0.00
MAR13086 MAM02847n -> MAM02847c ENSG00000030066 and ENSG00000047410 and ENSG00000058804 and ENSG00000069248 and ENSG00000075188 and ENSG00000085415 and ENSG00000093000 and ENSG00000094914 and ENSG00000095319 and ENSG00000101146 and ENSG00000102900 and ENSG00000108559 and ENSG00000110713 and ENSG00000111581 and ENSG00000113569 and ENSG00000119392 and ENSG00000120253 and ENSG00000124789 and ENSG00000125450 and ENSG00000126883 and ENSG00000132182 and ENSG00000136243 and ENSG00000138750 and ENSG00000139496 and ENSG00000153201 and ENSG00000153207 and ENSG00000155561 and ENSG00000157020 and ENSG00000157349 and ENSG00000163002 and ENSG00000196313 and ENSG00000213024 0.00 1000.00 0.00
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