The molecular mechanisms of Guizhi Fuling Pills in ameliorating Alzheimer's disease-like cognitive impairment: insights from transcriptomics, metabolomics, and gut microbiome.
The 2 matches
- [1] § Results › Network pharmacological analysis ↔ goatools/anno/broad_gos.py, lines 91–156 · score 0.78 · receptor activity, cellular components, molecular functions, positive regulation, membrane, compounds
- [2] § Materials and methods › Transcriptomics ↔ goatools/test_data/genes_NCBI_10090_All.py, lines 301–360 · score 0.52 · cDNA, mRNA, Plus, sequencing, Co, transcription
Paper
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The authors' code
Python · 158 lines · 14 KB · BSD-2-Clause · 1 match
- """List of the GO IDs that have lots of descendants and low information content"""
- __copyright__ = "Copyright (C) 2018-2019, DV Klopfenstein. All rights reserved."
- __author__ = "DV Klopfenstein"
- # pylint: disable=line-too-long
- NS2GOS_SHORT = {
- 'BP': {
- 'GO:0008150', # BP 29685 18,453 0.015902 4.14 L00 D00 biological_process
- 'GO:0065007', # BP 12809 12,729 0.010970 4.51 L01 D01 A biological regulation
- 'GO:0050789', # BP 11559 12,053 0.010387 4.57 L02 D02 A regulation of biological process
- 'GO:0009987', # BP 11246 15,270 0.013159 4.33 L01 D01 B cellular process
- 'GO:0050794', # BP 8212 11,011 0.009489 4.66 L03 D03 A regulation of cellular process
- 'GO:0008152', # BP 6394 8,835 0.007614 4.88 L01 D01 C metabolic process
- 'GO:0071704', # BP 6051 8,306 0.007158 4.94 L02 D02 C organic substance metabolic process
- 'GO:0044237', # BP 5691 7,989 0.006885 4.98 L02 D02 BC cellular metabolic process
- },
- 'CC':{
- 'GO:0005575', # CC 4197 19,578 0.059148 2.83 L00 D00 cellular_component
- 'GO:0044464', # CC 3298 17,521 0.052934 2.94 L01 D01 A cell part
- 'GO:0044424', # CC 2356 15,063 0.045508 3.09 L02 D02 A intracellular part
- },
- 'MF':{
- 'GO:0003674', # MF 11120 17,426 0.068263 2.68 L00 D00 molecular_function
- 'GO:0003824', # MF 7659 5,710 0.022368 3.80 L01 D01 A catalytic activity
- 'GO:0005488', # MF 1887 15,267 0.059805 2.82 L01 D01 B binding
- },
- }
- NS2GOS = {
- 'BP': {
- 'GO:0008150', # BP 29685 18,453 0.015902 4.14 L00 D00 biological_process
- 'GO:0065007', # BP 12809 12,729 0.010970 4.51 L01 D01 A biological regulation
- 'GO:0050789', # BP 11559 12,053 0.010387 4.57 L02 D02 A regulation of biological process
- 'GO:0009987', # BP 11246 15,270 0.013159 4.33 L01 D01 B cellular process
- 'GO:0050794', # BP 8212 11,011 0.009489 4.66 L03 D03 A regulation of cellular process
- 'GO:0008152', # BP 6394 8,835 0.007614 4.88 L01 D01 C metabolic process
- 'GO:0071704', # BP 6051 8,306 0.007158 4.94 L02 D02 C organic substance metabolic process
- 'GO:0044237', # BP 5691 7,989 0.006885 4.98 L02 D02 BC cellular metabolic process
- 'GO:0044238', # BP 4213 7,935 0.006838 4.99 L02 D02 C primary metabolic process
- 'GO:0006807', # BP 3954 7,465 0.006433 5.05 L02 D02 C nitrogen compound metabolic process
- 'GO:0048518', # BP 3575 6,212 0.005353 5.23 L03 D03 A positive regulation of biological process
- 'GO:0048519', # BP 3483 5,751 0.004956 5.31 L03 D03 A negative regulation of biological process
- 'GO:0019222', # BP 3356 7,289 0.006282 5.07 L03 D03 A regulation of metabolic process
- 'GO:0032502', # BP 3217 4,946 0.004262 5.46 L01 D01 D developmental process
- 'GO:0031323', # BP 2921 6,302 0.005431 5.22 L04 D04 A regulation of cellular metabolic process
- 'GO:1901564', # BP 2881 5,283 0.004553 5.39 L03 D03 C organonitrogen compound metabolic process
- 'GO:0051239', # BP 2674 3,248 0.002799 5.88 L03 D03 A regulation of multicellular organismal process
- 'GO:1901360', # BP 2602 3,753 0.003234 5.73 L03 D03 C organic cyclic compound metabolic process
- 'GO:0080090', # BP 2477 6,230 0.005369 5.23 L04 D04 A regulation of primary metabolic process
- 'GO:0048523', # BP 2396 4,843 0.004174 5.48 L04 D04 A negative regulation of cellular process
- 'GO:0043170', # BP 2385 6,619 0.005704 5.17 L03 D03 C macromolecule metabolic process
- 'GO:0048522', # BP 2378 5,479 0.004722 5.36 L04 D04 A positive regulation of cellular process
- 'GO:0048583', # BP 2372 4,334 0.003735 5.59 L03 D03 A regulation of response to stimulus
- 'GO:0044281', # BP 2364 1,744 0.001503 6.50 L02 D02 C small molecule metabolic process
- 'GO:0050896', # BP 2283 5,768 0.004971 5.30 L01 D01 E response to stimulus
- 'GO:0051171', # BP 2234 6,060 0.005222 5.25 L04 D04 A regulation of nitrogen compound metabolic process
- 'GO:0006725', # BP 2233 3,528 0.003040 5.80 L03 D03 BC cellular aromatic compound metabolic process
- 'GO:0034641', # BP 2155 3,827 0.003298 5.71 L03 D03 BC cellular nitrogen compound metabolic process
- 'GO:0046483', # BP 2152 3,483 0.003002 5.81 L03 D03 BC heterocycle metabolic process
- 'GO:0051179', # BP 2119 4,811 0.004146 5.49 L01 D01 F localization
- 'GO:0060255', # BP 2110 6,771 0.005835 5.14 L04 D04 A regulation of macromolecule metabolic process
- 'GO:0050793', # BP 2040 2,693 0.002321 6.07 L03 D03 A regulation of developmental process
- 'GO:0009058', # BP 1843 2,533 0.002183 6.13 L02 D02 C biosynthetic process
- 'GO:0032879', # BP 1798 2,851 0.002457 6.01 L03 D03 A regulation of localization
- 'GO:1901576', # BP 1766 2,475 0.002133 6.15 L03 D03 C organic substance biosynthetic process
- 'GO:0071840', # BP 1738 5,385 0.004641 5.37 L01 D01 G cellular component organization or biogenesis
- 'GO:0044260', # BP 1726 4,739 0.004084 5.50 L03 D04 BC cellular macromolecule metabolic process
- 'GO:0065008', # BP 1710 3,759 0.003239 5.73 L02 D02 A regulation of biological quality
- 'GO:0016043', # BP 1709 5,337 0.004599 5.38 L02 D02 BG cellular component organization
- 'GO:0051234', # BP 1681 4,325 0.003727 5.59 L02 D02 F establishment of localization
- 'GO:0006810', # BP 1587 4,195 0.003615 5.62 L03 D03 F transport
- 'GO:0009889', # BP 1583 4,400 0.003792 5.57 L04 D04 A regulation of biosynthetic process
- 'GO:0044249', # BP 1575 2,346 0.002022 6.20 L03 D03 BC cellular biosynthetic process
- 'GO:2000026', # BP 1532 2,154 0.001856 6.29 L04 D04 A regulation of multicellular organismal development
- 'GO:0006139', # BP 1524 3,312 0.002854 5.86 L03 D04 BC nucleobase-containing compound metabolic process
- 'GO:0051704', # BP 1474 1,534 0.001322 6.63 L01 D01 H multi-organism process
- 'GO:0031326', # BP 1467 4,321 0.003724 5.59 L05 D05 A regulation of cellular biosynthetic process
- 'GO:0009056', # BP 1382 1,946 0.001677 6.39 L02 D02 C catabolic process
- 'GO:0051128', # BP 1372 2,507 0.002160 6.14 L04 D04 A regulation of cellular component organization
- 'GO:0010646', # BP 1323 3,537 0.003048 5.79 L04 D04 A regulation of cell communication
- 'GO:0023051', # BP 1302 3,579 0.003084 5.78 L03 D03 A regulation of signaling
- 'GO:1901575', # BP 1290 1,678 0.001446 6.54 L03 D03 C organic substance catabolic process
- 'GO:0051049', # BP 1280 1,879 0.001619 6.43 L04 D04 A regulation of transport
- 'GO:0019538', # BP 1171 4,189 0.003610 5.62 L03 D04 C protein metabolic process
- 'GO:0044248', # BP 1164 1,693 0.001459 6.53 L03 D03 BC cellular catabolic process
- 'GO:0006082', # BP 1130 998 0.000860 7.06 L03 D03 BC organic acid metabolic process
- 'GO:0002682', # BP 1127 1,659 0.001430 6.55 L03 D03 A regulation of immune system process
- 'GO:0043436', # BP 1089 977 0.000842 7.08 L04 D04 BC oxoacid metabolic process
- 'GO:0048869', # BP 1062 2,764 0.002382 6.04 L02 D02 BD cellular developmental process
- 'GO:0042221', # BP 1059 2,723 0.002347 6.05 L02 D02 E response to chemical
- 'GO:0009893', # BP 1056 3,640 0.003137 5.76 L04 D04 A positive regulation of metabolic process
- 'GO:0043412', # BP 1048 3,230 0.002784 5.88 L04 D04 C macromolecule modification
- 'GO:0048856', # BP 1038 3,320 0.002861 5.86 L02 D02 D anatomical structure development
- 'GO:0009892', # BP 1035 3,414 0.002942 5.83 L04 D04 A negative regulation of metabolic process
- 'GO:0065009', # BP 1028 2,987 0.002574 5.96 L02 D02 A regulation of molecular function
- 'GO:0071702', # BP 1017 2,082 0.001794 6.32 L04 D04 F organic substance transport
- 'GO:0009966', # BP 1001 3,163 0.002726 5.90 L04 D05 A regulation of signal transduction
- 'GO:0032501', # BP 995 3,479 0.002998 5.81 L01 D01 I multicellular organismal process
- 'GO:0019219', # BP 987 4,138 0.003566 5.64 L05 D05 A regulation of nucleobase-containing compound metabolic process
- 'GO:0010556', # BP 970 4,134 0.003563 5.64 L05 D05 A regulation of macromolecule biosynthetic process
- 'GO:0044267', # BP 936 3,376 0.002909 5.84 L04 D05 BC cellular protein metabolic process
- 'GO:0031325', # BP 936 3,328 0.002868 5.85 L05 D05 A positive regulation of cellular metabolic process
- 'GO:0051246', # BP 936 2,935 0.002529 5.98 L05 D05 A regulation of protein metabolic process
- 'GO:0045595', # BP 921 1,876 0.001617 6.43 L04 D04 A regulation of cell differentiation
- 'GO:0036211', # BP 906 3,021 0.002603 5.95 L04 D05 C protein modification process
- 'GO:0006464', # BP 904 3,021 0.002603 5.95 L05 D06 BC cellular protein modification process
- 'GO:0006793', # BP 891 2,053 0.001769 6.34 L03 D03 BC phosphorus metabolic process
- 'GO:1901362', # BP 875 1,318 0.001136 6.78 L04 D04 C organic cyclic compound biosynthetic process
- 'GO:0031324', # BP 873 2,635 0.002271 6.09 L05 D05 A negative regulation of cellular metabolic process
- 'GO:0080134', # BP 855 1,644 0.001417 6.56 L04 D04 A regulation of response to stress
- 'GO:0010468', # BP 846 5,112 0.004405 5.42 L05 D05 A regulation of gene expression
- 'GO:0051716', # BP 846 2,935 0.002529 5.98 L02 D02 BE cellular response to stimulus
- 'GO:0022414', # BP 843 1,389 0.001197 6.73 L01 D01 J reproductive process
- 'GO:0090304', # BP 833 2,754 0.002373 6.04 L04 D05 BC nucleic acid metabolic process
- 'GO:0006796', # BP 828 2,026 0.001746 6.35 L04 D04 BC phosphate-containing compound metabolic process
- 'GO:0051240', # BP 828 1,797 0.001549 6.47 L04 D04 A positive regulation of multicellular organismal process
- 'GO:0048584', # BP 824 2,441 0.002104 6.16 L04 D04 A positive regulation of response to stimulus
- },
- 'CC':{
- 'GO:0005575', # CC 4197 19,578 0.059148 2.83 L00 D00 cellular_component
- 'GO:0044464', # CC 3298 17,521 0.052934 2.94 L01 D01 A cell part
- 'GO:0044424', # CC 2356 15,063 0.045508 3.09 L02 D02 A intracellular part
- 'GO:0032991', # CC 2107 6,150 0.018580 3.99 L01 D01 B protein-containing complex
- 'GO:0044422', # CC 1610 10,111 0.030547 3.49 L01 D01 C organelle part
- 'GO:0044446', # CC 1458 9,810 0.029638 3.52 L02 D03 AC intracellular organelle part
- 'GO:0044444', # CC 1257 9,735 0.029411 3.53 L03 D03 A cytoplasmic part
- 'GO:0044425', # CC 908 6,938 0.020961 3.87 L01 D01 D membrane part
- 'GO:0044428', # CC 490 5,022 0.015172 4.19 L03 D04 AC nuclear part
- 'GO:0044459', # CC 472 2,985 0.009018 4.71 L02 D02 AD plasma membrane part
- 'GO:0043226', # CC 383 11,684 0.035299 3.34 L01 D01 E organelle
- },
- 'MF':{
- 'GO:0003674', # MF 11120 17,426 0.068263 2.68 L00 D00 molecular_function
- 'GO:0003824', # MF 7659 5,710 0.022368 3.80 L01 D01 A catalytic activity
- 'GO:0016740', # MF 2457 2,272 0.008900 4.72 L02 D02 A transferase activity
- 'GO:0016491', # MF 2368 748 0.002930 5.83 L02 D02 A oxidoreductase activity
- 'GO:0005488', # MF 1887 15,267 0.059805 2.82 L01 D01 B binding
- 'GO:0016787', # MF 1643 2,533 0.009923 4.61 L02 D02 A hydrolase activity
- 'GO:0005215', # MF 1079 1,140 0.004466 5.41 L01 D01 C transporter activity
- 'GO:0022857', # MF 1042 1,045 0.004094 5.50 L02 D02 C transmembrane transporter activity
- 'GO:0005515', # MF 966 11,807 0.046252 3.07 L02 D02 B protein binding
- 'GO:0015075', # MF 691 880 0.003447 5.67 L03 D03 C ion transmembrane transporter activity
- 'GO:0015318', # MF 635 817 0.003200 5.74 L03 D03 C inorganic molecular entity transmembrane transporter activity
- 'GO:0016772', # MF 603 918 0.003596 5.63 L03 D03 A transferase activity, transferring phosphorus-containing groups
- 'GO:0016788', # MF 558 741 0.002903 5.84 L03 D03 A hydrolase activity, acting on ester bonds
- 'GO:0097159', # MF 497 6,328 0.024789 3.70 L02 D02 B organic cyclic compound binding
- 'GO:1901363', # MF 457 6,241 0.024448 3.71 L02 D02 B heterocyclic compound binding
- 'GO:0140096', # MF 443 2,165 0.008481 4.77 L02 D02 A catalytic activity, acting on a protein
- 'GO:0005102', # MF 431 1,624 0.006362 5.06 L03 D03 B signaling receptor binding
- 'GO:0060089', # MF 419 1,538 0.006025 5.11 L01 D01 D molecular transducer activity
- 'GO:0038023', # MF 403 1,484 0.005813 5.15 L02 D02 D signaling receptor activity
- 'GO:0016301', # MF 355 762 0.002985 5.81 L04 D04 A kinase activity
- },
- }
- # Copyright (C) 2018-2019, DV Klopfenstein. All rights reserved
broad_gos.py at commit 4cd1c71, under BSD-2-Clause · at the source
Overview
- Wenzhou TCM Hospital of Zhejiang Chinese Medical University, Wenzhou, China
- Nanning Hospital of Traditional Chinese Medicine, Nanning, China
- Zhejiang Chinese Medical University, Hangzhou, China
Abstract
Background: Alzheimer’s disease (AD)-like cognitive impairment, as a major type of cognitive disorder, has witnessed a sharp rise in prevalence. Therefore, there is an urgent need to develop effective therapeutic intervention measures. Guizhi Fuling Pills (GFP), a classical Traditional Chinese Medicine (TCM) formula, has been shown to exert protective effects on cognitive function. However, its underlying mechanisms remain unclear.
Objective: To investigate the effects of GFP on AD-like cognitive impairment and elucidate its underlying mechanisms.
Methods: D-galactose (D-gal)-induced aged mice were used as the model. Mice were administered via gavage for 4 weeks with 0.9% normal saline (0.1 mL/
Results: Guizhi Fuling Pills improved learning and memory function in aged mice, ameliorated hippocampal neuronal morphology, and reduced p-Tau protein deposition. Network pharmacology and hippocampal transcriptomic analyses suggested that the active components in GFP may ameliorate cognitive impairment through multiple mechanisms. It included regulation of the VEGF and PI3K/
Conclusion: The findings of this study suggest that GFP may ameliorate cognitive dysfunction in AD-like cognitive impairment mice through multiple mechanisms, including repair of the BBB, attenuation of inflammatory responses, and modulation of the gut microbiota and metabolic disorders.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repositories
Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.
OpenGene/fastp
8a2397b6628ae14127efdb7566f67fc05f9aea56, 10 September 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
68 files
- parallel.py, Python, 592 lines
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bench_e2e.sh , Shell, 238 lines - scripts/
test_issue_697_stdout_me , Shell, 28 linesrge.sh - src/
adaptertrimmer.cpp , C++, 185 lines - src/
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common.h , C/C++, 67 lines - src/
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evaluator.cpp , C++, 633 lines - src/
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fastareader.cpp , C++, 120 lines - src/
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writerthread.h , C/C++, 68 lines - LICENSE, License, 21 lines
- README.md, Text, 558 lines
tanghaibao/GOatools
4cd1c71bca876d545c2a7e8714ac907019e0649c, 21 August 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
136 files
- docs/
descendants_with_relatio , Python, 109 linesnships_example.py - goatools/
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anno/ , Python, 4 lines__init__.py - goatools/
anno/ , Python, 385 linesannoreader_base.py - goatools/
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Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 200 scripts, each with its path and the digest of its content;
- 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data availability statement
The datasets presented in this study can be found in online repositories. The names of the repository/
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 9 authors, 5 keywords, 29 references.
Cite
This paper
Ma, L., Wang, J., Xu, Z., Huang, Z., Chen, K., Teng, X., Chen, M., Lin, S., & Zhou, R. (2026). The molecular mechanisms of Guizhi Fuling Pills in ameliorating Alzheimer's disease-like cognitive impairment: insights from transcriptomics, metabolomics, and gut microbiome. Frontiers in aging neuroscience, 18, 1839445. https://
BibTeX
@article{ma2026molecular
author = {Ma, Lan and Wang, Jing and Xu, Zhenghao and Huang, Zuxiu and Chen, Kelong and Teng, Xiaoqiong and Chen, Miao and Lin, Shuyang and Zhou, Rong},
title = {{The molecular mechanisms of Guizhi Fuling Pills in ameliorating Alzheimer's disease-like cognitive impairment: insights from transcriptomics, metabolomics, and gut microbiome}},
journal = {Frontiers in aging neuroscience},
year = {2026},
month = aug,
volume = {18},
pages = {1839445},
publisher = {Frontiers Media SA},
issn = {1663-4365},
doi = {10.3389/
url = {https://
pmid = {42661899},
pmcid = {PMC13518511}
}
RIS
TY - JOUR
AU - Ma, Lan
AU - Wang, Jing
AU - Xu, Zhenghao
AU - Huang, Zuxiu
AU - Chen, Kelong
AU - Teng, Xiaoqiong
AU - Chen, Miao
AU - Lin, Shuyang
AU - Zhou, Rong
TI - The molecular mechanisms of Guizhi Fuling Pills in ameliorating Alzheimer's disease-like cognitive impairment: insights from transcriptomics, metabolomics, and gut microbiome
T2 - Frontiers in aging neuroscience
J2 - Front Aging Neurosci
PY - 2026
DA - 2026/
VL - 18
SP - 1839445
SN - 1663-4365
PB - Frontiers Media SA
DO - 10.3389/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.3389/
"type": "article-journal",
"title": "The molecular mechanisms of Guizhi Fuling Pills in ameliorating Alzheimer's disease-like cognitive impairment: insights from transcriptomics, metabolomics, and gut microbiome",
"container-title": "Frontiers in aging neuroscience",
"author": [
{
"family": "Ma",
"given": "Lan"
},
{
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},
{
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"given": "Zhenghao"
},
{
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},
{
"family": "Chen",
"given": "Kelong"
},
{
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},
{
"family": "Chen",
"given": "Miao"
},
{
"family": "Lin",
"given": "Shuyang"
},
{
"family": "Zhou",
"given": "Rong"
}
],
"container-title-short":
"volume": "18",
"page": "1839445",
"DOI": "10.3389/
"PMID": "42661899",
"PMCID": "PMC13518511",
"ISSN": "1663-4365",
"publisher": "Frontiers Media SA",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
8,
13
]
]
}
}
The tracing map gets a citation of its own once an author has validated it and it has a DOI.
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