ImageGP: An easy‐to‐use data visualization web server for scientific researchers

Chen, Tong; Liu, Yong‐Xin; Huang, Luqi

doi:10.1002/imt2.5

Cited by 277 publications

(180 citation statements)

References 17 publications

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“…The KEGG pathway analysis suggested that the genes are predominantly involved in different cancer pathways, development of bladder cancer, oncogenic virus infection pathways and so on. These findings again signify that the PSMC family genes may be associated with LUAD development and progression since the deregulation of the activity of PSMC s’ co-expressed genes in LUAD tissues can result in the initiation of oncogenic processes [42]. As a result, the co-expressed genes of the PSMC s could also be investigated in LUAD therapeutic and diagnostic measures discovery.…”

Section: Discussionmentioning

confidence: 85%

Identifying Proteasome 26S Subunit, ATPase (PSMC) Family Genes as the Prognostic Indicators and Therapeutic Targets in Lung Adenocarcinoma

Ullah

Islam

Moin

et al. 2022

Preprint

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This study explored the prognostic and therapeutic potentials of multiple Proteasome 26S Subunit, ATPase (PSMC) family of genes (PSMC1-5) in lung adenocarcinoma (LUAD) diagnosis and treatment. All the PSMCs were found to be differentially expressed (upregulated) at the mRNA and protein levels in LUAD tissues. The promoter and multiple coding regions of PSMCs were reported to be differentially and distinctly methylated, which may serve in the methylation-sensitive diagnosis of LUAD patients. Multiple somatic mutations (alteration frequency: 0.6-2%) were observed along the PSMCs coding regions in LUAD tissues that could assist in the high-throughput screening of LUAD patients. A significant association between PSMCs overexpression and LUAD patients’ poor overall and relapse-free survival (p<0.05, HR:>1.3) and individual cancer stages (p<0.001) was discovered, which justifies PSMCs as the ideal targets for LUAD diagnosis. Multiple immune cells and modulators (i.e., CD274, IDO1) were found to be associated with PSMCs expression in LUAD tissues that could aid in formulating PSMC-based diagnostic measures and therapeutic interventions for LUAD. Functional enrichment analysis of neighbor genes of PSMCs in LUAD tissues revealed different genes (i.e., SLIRP, PSMA2, NUDSF3) previously known to be involved in oncogenic processes and metastasis co-expressed with PSMCs, which could also be investigated further. Overall, this study recommends that PSMCs and their transcriptional and translational products are potential candidates for LUAD diagnostic and therapeutic measure discovery. However, further laboratory research is needed to validate the findings of this experiment.

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Section: Discussionmentioning

confidence: 85%

Identifying Proteasome 26S Subunit, ATPase (PSMC) Family Genes as the Prognostic Indicators and Therapeutic Targets in Lung Adenocarcinoma

Ullah

Islam

Moin

et al. 2022

Preprint

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“…All R packages were installed via Bioconductor (version 1.30.16) [ 20 ]. Overlapping diagrams were produced by VennDiagrams pot ( , accessed around 13 April 2022) [ 21 ].…”

Section: Methodsmentioning

confidence: 99%

Crosstalk between the Circadian Clock and Histone Methylation

Sun

Liu

et al. 2022

IJMS

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The circadian clock and histone modifications could form a feedback loop in Arabidopsis; whether a similar regulatory mechanism exists in rice is still unknown. Previously, we reported that SDG724 and OsLHY are two rice heading date regulators in rice. SDG724 encodes a histone H3K36 methyltransferase, and OsLHY is a vital circadian rhythm transcription factor. Both could be involved in transcription regulatory mechanisms and could affect gene expression in various pathways. To explore the crosstalk between the circadian clock and histone methylation in rice, we studied the relationship between OsLHY and SDG724 via the transcriptome analysis of their single and double mutants, oslhy, sdg724, and oslhysdg724. Screening of overlapped DEGs and KEGG pathways between OsLHY and SDG724 revealed that they could control many overlapped pathways indirectly. Furthermore, we identified three candidate targets (OsGI, OsCCT38, and OsPRR95) of OsLHY and one candidate target (OsCRY1a) of SDG724 in the clock pathway. Our results showed a regulatory relationship between OsLHY and SDG724, which paved the way for revealing the interaction between the circadian clock and histone H3K36 methylation.

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“…The Nearest Sequenced Taxon Index (NSTI) score was determined for each sample to evaluate the prediction accuracy of PICRUSt [ 54 ], and a lower value (roughly < 0.06) indicated that the functional profiles obtained were closely related to the reference genome. PCA was employed to group or separate samples using ImageGP [ 55 ] based on the function abundance of KEGG pathways on three levels. Significantly different KEGG pathways on level II between two salinity clusters were determined by Statistical Analysis of Metagenomic Profiles (STAMP) [ 56 ], using two-sided Welch’s t test with a Storey (normal distribution) or Benjamini–Hochberg (abnormal distribution) FDR multiple testing correction [ 57 ] (adjusted q value < 0.05).…”

Section: Methodsmentioning

confidence: 99%

Bacterial and Protistan Community Variation across the Changjiang Estuary to the Ocean with Multiple Environmental Gradients

Jiang

Zhu

et al. 2022

Microorganisms

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Plankton microorganisms play central roles in the marine food web and global biogeochemical cycles, while their distribution and abundance are affected by environmental variables. The determinants of microbial community composition and diversity in estuaries and surrounding waters with multiple environmental gradients at a fine scale remain largely unclear. Here, we investigated bacterial and protistan community assembly in surface waters from 27 stations across the Changjiang Estuary to the ocean, with salinity ranging from 0 to 32.1, using 16S rRNA and 18S rRNA gene amplicon sequencing. Statistical analyses revealed that salinity is the major factor structuring both bacterial and protistan communities. Salinity also acted as a significant environmental determinant influencing alpha-diversity patterns. Alpha diversity indices for bacterial and protistan communities revealed a species minimum in higher-salinity waters (22.1–32.1). Contrary to the protistan community, the highest bacterial diversity was identified in medium-salinity waters (2.8–18.8), contrasting Remane’s Artenminimum concept. The distribution of major planktonic taxa followed the expected pattern, and the salinity boundary for Syndiniales was specifically identified. These findings revealed the significant effects of salinity on the microbial community across an estuary to ocean transect and the distinct response to salinity between bacterial and protistan communities.

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ImageGP: An easy‐to‐use data visualization web server for scientific researchers

Cited by 277 publications

References 17 publications

Identifying Proteasome 26S Subunit, ATPase (PSMC) Family Genes as the Prognostic Indicators and Therapeutic Targets in Lung Adenocarcinoma

Identifying Proteasome 26S Subunit, ATPase (PSMC) Family Genes as the Prognostic Indicators and Therapeutic Targets in Lung Adenocarcinoma

Crosstalk between the Circadian Clock and Histone Methylation

Bacterial and Protistan Community Variation across the Changjiang Estuary to the Ocean with Multiple Environmental Gradients

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