cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6681443.v1
title: Identification of Epigenetic Modulators in Human Breast Cancer by Integrated Analysis of DNA Methylation and RNA-Seq Data

description: Human tumors undergo massive changes in DNA methylation. Recent studies showed that site-specific methylation of CpG sites is determined by the DNA sequence context surrounding the CpG site, which alludes to a possible mechanism for site-specific aberrant DNA methylation in cancer through DNA-binding proteins. In this paper, DNA methylation data and RNA-Seq data of breast tumors and normal tissues in the database of The Cancer Genome Atlas (TCGA) were integrated with information of DNA motifs in seven databases to find DNA-binding proteins and their binding motifs that were involved in aberrant DNA methylation in breast cancer. A total of 42,850 differentially methylated regions (DMRs) that include 77,298 CpG sites were detected in breast cancer. One hundred eight DNA motifs were found to be enriched in DMRs, and 109 genes encoding proteins binding to these motifs were determined. Based on these motifs and genes, 63 methylation modulator genes were identified to regulate differentially methylated CpG sites in breast cancer. A network of these 63 modulator genes and 645 transcription factors was constructed, and 20 network modules were determined. A number of pathways and gene sets related to breast cancer were found to be enriched in these network modules. The 63 methylation modulator genes identified may play an important role in aberrant methylation of CpG sites in breast cancer. They may help to understand site-specific dysregulation of DNA methylation and provide epigenetic markers for breast cancer.
DOI: 10.6084/m9.figshare.20306707.v1
title: Additional file 2 of Quantitative proteomics analysis to assess protein expression levels in the ovaries of pubescent goats

description: Additional file 2.
DOI: 10.34740/kaggle/dsv/7666025
title: Top Spotify Songs in 73 Countries (Daily Updated)
DOI: 10.5517/ccdc.csd.cc28gly9
title: CCDC 2099411: Experimental Crystal Structure Determination

description: Related Article: Aniffa Kouton, Robert Pepin, Nicholas Alexander Maciulis, Xinfeng Gao, Veronica Carta, Allen R. Siedle|2024|ACS Omega|9|5395|doi:10.1021/acsomega.3c06550
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fp5dq
title: CCDC 2254673: Experimental Crystal Structure Determination

description: Related Article: Ming Li, Li Shao, Zhongwen Liu, Rui Liu, Ivan I. Stoikov, Niveen M. Khashab, Bin Hua, Feihe Huang|2024|ACS Applied Materials and Interfaces|16|6614|doi:10.1021/acsami.3c15729
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2frq42
title: CCDC 2257114: Experimental Crystal Structure Determination

description: Related Article: Min Chen, Longqing Yang, Yuzhen Li, Yinhe Qu, Guihua Pan, Xiaoming Feng, Xiaohua Liu |2023|Sci.China.Chem.|67|542|doi:10.1007/s11426-023-1794-2
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.7730063.v1
title: Additional file 6: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Conserved amino acids and numbers in the Helix1, 2, 3 which were from the GT domain of TaGTs, BdGTs and OsGTs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7730060.v1
title: Additional file 1: of Genome-wide analysis and identification of the low potassium stress responsive gene SiMYB3 in foxtail millet (Setariaitalica L.)

description: Table S1. List of the primers used in qRT-PCR analyses. Table S2. List of all genes showing transcriptional changes during Kâ +â â deficiency. Table S3. The differentially expressed genes (1982 genes) for the K+ deficient stress in foxtail millet. Table S4. Gene ontology (GO) classification of the differentially expressed genes. Table S5. Detail of differentially expressed transcription factors. Table S6. List of 248 differentially expressed genes common for potassium deprivation among millet, rice and Arabidopsis. Table S7. List of 1734 specifically expressed genes in foxtail millet for potassium deprivation. (XLSX 3089 kb)
DOI: 10.6084/m9.figshare.22638844.v1
title: Network pharmacology-integrated molecular docking analysis of phytocompounds of <i>Caesalpinia pulcherrima</i> (peacock flower) as potential anti-metastatic agents

description: <i>Caesalpinia pulcherrima,</i> or peacock flower, has been a subject of cancer therapeutics research, showing promising anti-cancer and anti-metastatic properties. The present research aims to investigate the anti-metastatic potential of the flower, through bioinformatics approaches. Metastasis targets numbering 471 were identified through overlap analysis following NCBI gene, Gene Card and OMIM query. Phytocompounds of the flower were retrieved from PubChem and their protein interactions predicted using Super-PRED and TargetNet. The 28 targets that overlapped with the predicted proteins were used to generate STRING &gt;0.7. Enrichment analysis revealed that <i>C. pulcherrima</i> may inhibit metastasis through angiogenesis-related and leukocyte migration-related pathways. HSP90AA1, ESR1, PIK3CA, ERBB2, KDR and MMP9 were identified as potential core targets while and 6 compounds (3-[(4-Hydroxyphenyl)methylidene]-7,8-dimethoxychromen-4-one (163076213), clotrimazole (2812), Isovouacapenol A (636673), [(4aR,5R,6aS,7R,11aS,11bR)-4a-hydroxy-4,4,7,11b-tetramethyl-9-oxo-1,2,3,5,6,6a,7,11a-octahydronaphtho[2,1-f][1]benzofuran-5-yl] benzoate (163104827), Stigmast-5-en-3beta-ol (86821) and 4,2'-dihydroxy-4'-methoxychalcone (592216)) were identified as potential core compounds. Molecular docking analysis and molecular dynamics simulations investigations revealed that ERBB2, HSP90AA1 and KDR, along with the newly discovered 163076213 compound to be the most significant metastasis targets and bioactive compound, respectively. These three core targets demonstrated interactions consistent with angiogenesis and leukocyte migration pathways. Furthermore, potentially novel interactions, such as KDR-MMP9, KDR-PIK3CA, ERBB2-HSP90AA1, ERBB2-ESR1, ERBB2-PIK3CA and ERBB2-MMP9 interactions were identified and may play a role in crosslinking the aforementioned metastatic pathways. Therefore, the present study revealed the main mechanisms behind the anti-metastatic effects of <i>C. pulcherrima</i>, paving the path for further research on these compounds and proteins to accelerate the research of cancer therapeutics and application of <i>C. pulcherrima.</i> Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22638844
title: Network pharmacology-integrated molecular docking analysis of phytocompounds of <i>Caesalpinia pulcherrima</i> (peacock flower) as potential anti-metastatic agents

description: <i>Caesalpinia pulcherrima,</i> or peacock flower, has been a subject of cancer therapeutics research, showing promising anti-cancer and anti-metastatic properties. The present research aims to investigate the anti-metastatic potential of the flower, through bioinformatics approaches. Metastasis targets numbering 471 were identified through overlap analysis following NCBI gene, Gene Card and OMIM query. Phytocompounds of the flower were retrieved from PubChem and their protein interactions predicted using Super-PRED and TargetNet. The 28 targets that overlapped with the predicted proteins were used to generate STRING &gt;0.7. Enrichment analysis revealed that <i>C. pulcherrima</i> may inhibit metastasis through angiogenesis-related and leukocyte migration-related pathways. HSP90AA1, ESR1, PIK3CA, ERBB2, KDR and MMP9 were identified as potential core targets while and 6 compounds (3-[(4-Hydroxyphenyl)methylidene]-7,8-dimethoxychromen-4-one (163076213), clotrimazole (2812), Isovouacapenol A (636673), [(4aR,5R,6aS,7R,11aS,11bR)-4a-hydroxy-4,4,7,11b-tetramethyl-9-oxo-1,2,3,5,6,6a,7,11a-octahydronaphtho[2,1-f][1]benzofuran-5-yl] benzoate (163104827), Stigmast-5-en-3beta-ol (86821) and 4,2'-dihydroxy-4'-methoxychalcone (592216)) were identified as potential core compounds. Molecular docking analysis and molecular dynamics simulations investigations revealed that ERBB2, HSP90AA1 and KDR, along with the newly discovered 163076213 compound to be the most significant metastasis targets and bioactive compound, respectively. These three core targets demonstrated interactions consistent with angiogenesis and leukocyte migration pathways. Furthermore, potentially novel interactions, such as KDR-MMP9, KDR-PIK3CA, ERBB2-HSP90AA1, ERBB2-ESR1, ERBB2-PIK3CA and ERBB2-MMP9 interactions were identified and may play a role in crosslinking the aforementioned metastatic pathways. Therefore, the present study revealed the main mechanisms behind the anti-metastatic effects of <i>C. pulcherrima</i>, paving the path for further research on these compounds and proteins to accelerate the research of cancer therapeutics and application of <i>C. pulcherrima.</i> Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22709799
title: Molecular mechanisms of Chengshi Beixie Fenqing Decoction based on network pharmacology: pivotal roles of relaxin signaling pathway and its associated target proteins against Benign prostatic hyperplasia

description: Benign prostatic hyperplasia (BPH) is a common disease that affects the quality of life of middle-aged and older men. We investigated the therapeutical effects of Chengshi Beixie Fenqing Decoction (CBFD), a classic traditional Chinese medicine prescription, on BPH through <i>in vivo</i> model and network pharmacology. Bioactives in CBFD were detected through UPLC-Q-Tof-MS/MS and GC-MS, and filtered by the modified Lipinski’s rule. Target proteins associated with the filtered compounds and BPH are selected from public databases. Venn diagram identified the overlapping target proteins between the bioactives-interacted target proteins and the BPH-targeted proteins. The bioactive-protein interactive networking of BPH was analyzed through the KEGG pathway on STRING to identify potential ligand-target and visualized the rich factors on the R packet. After that, the molecular docking test (MDT) was performed between bioactives and target proteins. It showed that the mechanism of CBFD against BPH was related to 104 signaling pathways of 42 compounds. AKT1, 6-demethyl-4′-methyl-<i>N</i>-methylcoclaurine and relaxin signaling pathways were selected as a hub target, key bioactivitie and hub signaling pathway, respectively. In addition, three major compounds, 6-demethyl-4′-methyl-<i>N</i>-methylcoclaurine, isoliensinine and liensinine, had the highest affinity on MDT for the three crucial target proteins, AKT1, JUN and MAPK1. These proteins were associated with the relaxin signaling pathway, which regulated the level of nitric oxide and is implicated in both BPH development and CBFD. We concluded that the three key bioactivities found in Plumula nelumbinis of CBFD may contribute to improving BPH condition by activating the relaxin signaling pathways. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22709799.v1
title: Molecular mechanisms of Chengshi Beixie Fenqing Decoction based on network pharmacology: pivotal roles of relaxin signaling pathway and its associated target proteins against Benign prostatic hyperplasia

description: Benign prostatic hyperplasia (BPH) is a common disease that affects the quality of life of middle-aged and older men. We investigated the therapeutical effects of Chengshi Beixie Fenqing Decoction (CBFD), a classic traditional Chinese medicine prescription, on BPH through <i>in vivo</i> model and network pharmacology. Bioactives in CBFD were detected through UPLC-Q-Tof-MS/MS and GC-MS, and filtered by the modified Lipinski’s rule. Target proteins associated with the filtered compounds and BPH are selected from public databases. Venn diagram identified the overlapping target proteins between the bioactives-interacted target proteins and the BPH-targeted proteins. The bioactive-protein interactive networking of BPH was analyzed through the KEGG pathway on STRING to identify potential ligand-target and visualized the rich factors on the R packet. After that, the molecular docking test (MDT) was performed between bioactives and target proteins. It showed that the mechanism of CBFD against BPH was related to 104 signaling pathways of 42 compounds. AKT1, 6-demethyl-4′-methyl-<i>N</i>-methylcoclaurine and relaxin signaling pathways were selected as a hub target, key bioactivitie and hub signaling pathway, respectively. In addition, three major compounds, 6-demethyl-4′-methyl-<i>N</i>-methylcoclaurine, isoliensinine and liensinine, had the highest affinity on MDT for the three crucial target proteins, AKT1, JUN and MAPK1. These proteins were associated with the relaxin signaling pathway, which regulated the level of nitric oxide and is implicated in both BPH development and CBFD. We concluded that the three key bioactivities found in Plumula nelumbinis of CBFD may contribute to improving BPH condition by activating the relaxin signaling pathways. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22710378.v1
title: Discovering potential inhibitors of Raf proto-oncogene serine/threonine kinase 1: a virtual screening approach towards anticancer drug development

description: Raf proto-oncogene serine/threonine kinase 1 (RAF1 or c-Raf) is a serine/threonine protein kinase crucial in regulating cell growth, differentiation, and survival. Any disruption or overexpression of RAF1 can result in neoplastic transformation and other disorders such as cardiomyopathy, Noonan syndrome, leopard syndrome, etc. RAF1 has been identified as a potential therapeutic target in drug development against various complex diseases, including cancer, due to its remarkable role in disease progression. Here, we carried out a multitier virtual screening study involving different <i>in-silico</i> approaches to discover potential inhibitors of RAF1. After applying the Lipinski rule of five, we retrieved all phytocompounds from the IMPPAT database based on their physicochemical properties. We performed a molecular docking-based virtual screening and got top hits with the best binding affinity and ligand efficiency. Then we screened out the selected hits using the PAINS filter, ADMET properties, and other druglike features. Eventually, PASS evaluation identifies two phytocompounds, Moracin C and Tectochrysin, with appreciable anti-cancerous properties. Finally, all-atom molecular dynamics simulation (MDS) followed by interaction analysis was performed on the elucidated compounds in complex with RAF1 for 200 ns to investigate their time-evolution dynamics and interaction mechanism. Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) and Dynamical Cross-Correlation Matrix (DCCM) analyses then followed these results from the simulated trajectories. According to the results, the elucidated compounds stabilize the RAF1 structure and lead to fewer conformational alterations. The results of the current study indicated that Moracin C and Tectochrysin could serve as potential inhibitors of RAF1 after required validation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22731199
title: In silico designing a novel TLR4-mediating multiepitope vaccine against monkeypox <i>via</i> advanced immunoinformatics and bioinformatics approaches

description: Monkeypox virus is a member of <i>the Poxviridae</i> family, which causes monkeypox zoonotic disease. Since July 2022, the prevention of monkeypox have become more considerable due to the new outbreak, making it a global concern. Therefore, we used an in silico-based method, including immunoinformatics, bioinformatics, molecular docking, and gene cloning approaches to design a novel multiepitope vaccine against monkeypox. Three immunogenic envelope proteins of monkeypox virus, including G10R, E8L, and A30L, were selected to predict appropriate immune system stimulator epitopes. The A30L is common between smallpox and monkeypox virus, so the proposed vaccine may be effective against smallpox too. There is no evidence of allergenicity and toxicity of the vaccine epitopes. To boost the immunogenicity of the designed vaccine, we used the helper epitope of PADRE and RS01as adjuvants. Furthermore, some linkers are used to link epitopes and adjuvants together. The physicochemical futures of the designed vaccine were assessed. The tertiary structure of the vaccine was modeled and then refined to improve its structure and physicochemical properties. To analyze the vaccine construct and TLR4 complex affinity, they were docked to gather. Besides, the vaccine was cloned into E.coli. pET-21b(+) plasmid to reveal that it can be expressed and stimulate the immune system. Immune stimulation evaluation showed that the candidate vaccine could induce the production of IgM, IgG1, and IgG2 antibodies. Overall, we suggested an effective vaccine candidate against monkeypox. However, Future studies and clinical trials should be done to ensure the efficacy and safety of this vaccine. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22731199.v1
title: In silico designing a novel TLR4-mediating multiepitope vaccine against monkeypox <i>via</i> advanced immunoinformatics and bioinformatics approaches

description: Monkeypox virus is a member of <i>the Poxviridae</i> family, which causes monkeypox zoonotic disease. Since July 2022, the prevention of monkeypox have become more considerable due to the new outbreak, making it a global concern. Therefore, we used an in silico-based method, including immunoinformatics, bioinformatics, molecular docking, and gene cloning approaches to design a novel multiepitope vaccine against monkeypox. Three immunogenic envelope proteins of monkeypox virus, including G10R, E8L, and A30L, were selected to predict appropriate immune system stimulator epitopes. The A30L is common between smallpox and monkeypox virus, so the proposed vaccine may be effective against smallpox too. There is no evidence of allergenicity and toxicity of the vaccine epitopes. To boost the immunogenicity of the designed vaccine, we used the helper epitope of PADRE and RS01as adjuvants. Furthermore, some linkers are used to link epitopes and adjuvants together. The physicochemical futures of the designed vaccine were assessed. The tertiary structure of the vaccine was modeled and then refined to improve its structure and physicochemical properties. To analyze the vaccine construct and TLR4 complex affinity, they were docked to gather. Besides, the vaccine was cloned into E.coli. pET-21b(+) plasmid to reveal that it can be expressed and stimulate the immune system. Immune stimulation evaluation showed that the candidate vaccine could induce the production of IgM, IgG1, and IgG2 antibodies. Overall, we suggested an effective vaccine candidate against monkeypox. However, Future studies and clinical trials should be done to ensure the efficacy and safety of this vaccine. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7730045.v1
title: Additional file 33: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Raw data (including DNA sequences and amino acids) of TaGT and BdGT genes sequences. (FA 396 kb)
DOI: 10.7910/dvn/hl2l86/fsmgem
title: 3-Chen_Lu_Machine Learning for COVID-19_Literature Review.pptx

description: :unav
DOI: 10.6084/m9.figshare.7730060
title: Additional file 1: of Genome-wide analysis and identification of the low potassium stress responsive gene SiMYB3 in foxtail millet (Setariaitalica L.)

description: Table S1. List of the primers used in qRT-PCR analyses. Table S2. List of all genes showing transcriptional changes during Kâ +â â deficiency. Table S3. The differentially expressed genes (1982 genes) for the K+ deficient stress in foxtail millet. Table S4. Gene ontology (GO) classification of the differentially expressed genes. Table S5. Detail of differentially expressed transcription factors. Table S6. List of 248 differentially expressed genes common for potassium deprivation among millet, rice and Arabidopsis. Table S7. List of 1734 specifically expressed genes in foxtail millet for potassium deprivation. (XLSX 3089 kb)
DOI: 10.6084/m9.figshare.7730063
title: Additional file 6: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Conserved amino acids and numbers in the Helix1, 2, 3 which were from the GT domain of TaGTs, BdGTs and OsGTs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7730069
title: Additional file 7: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Representing number of Trihelix genes present in different plant species. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7729889.v1
title: Additional file 11: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: The cis-elements in promoter sequences of Trihelix genes in B. distachyon. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.7729895.v1
title: Additional file 12: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: The promoter regions of TaGT and BdGT genes contained plant growth/development - and stress response-related cis-elements. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.7729889
title: Additional file 11: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: The cis-elements in promoter sequences of Trihelix genes in B. distachyon. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.11924403
title: Additional file 1 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 1: Table S1. The epicardial adipose tissue (EAT) development was correlated with pathways based on time series-related GSEA.
DOI: 10.6084/m9.figshare.15064018
title: Additional file 9 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 9: Table S5. The GO and KEGG analyses of down-regulated DEmiRNAs in fetus vs. child group.
DOI: 10.6084/m9.figshare.15064018.v1
title: Additional file 9 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 9: Table S5. The GO and KEGG analyses of down-regulated DEmiRNAs in fetus vs. child group.
DOI: 10.6084/m9.figshare.20306713
title: Additional file 4 of Quantitative proteomics analysis to assess protein expression levels in the ovaries of pubescent goats

description: Additional file 4.
DOI: 10.6084/m9.figshare.11924427.v1
title: Additional file 5 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 5: Table S5. The competing endogenous RNA (ceRNA) regulatory network construction.
DOI: 10.6084/m9.figshare.20306704
title: Additional file 1 of Quantitative proteomics analysis to assess protein expression levels in the ovaries of pubescent goats

description: Additional file 1.