Direct Data-independent acquisition proteome of the intestinal regenerative tissue of sea cucumbers
Ontology highlight
ABSTRACT:
ORGANISM(S): Apostichopus Japonicus
SUBMITTER: 
Chenghua Li
PROVIDER: PXD057001 | iProX | Mon Oct 21 00:00:00 GMT+01:00 2024
REPOSITORIES: iProX
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Project description:Based on the Raw files obtained by mass spectrometry detection, 1) Construct a sample-specific protein database according to the source of the samples, and then conduct database search using analysis software; 2) Conduct quality control analysis at the peptide and protein levels based on the results of database search; 3) Conduct quantitative analysis of proteins, including quantitative distribution and repeatability analysis; 4) Perform common functional annotations on the identified proteins, including GO, KEGG, Protein domain, COG/KOG, STRING database annotations, etc. 6) Functional classification statistical analysis of proteins between the two groups was conducted, including GO secondary classification, subcellular localization classification, COG/KOG classification and KEGG pathway classification statistics; 7) The Fisher's exact test method was used to conduct enrichment analysis on the differentially expressed proteins between the two groups, involving the functions of GO, KEGG and Protein domain; 8) When the project has multiple experimental groups, the functional relationships of differentially expressed proteins under different experimental conditions are compared through rich cluster analysis. 9) Through Protein-protein interaction network (PPI) analysis, the key regulatory proteins under specific experimental conditions were screened out.
2026-06-15 | PXD063853 | Pride
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:Purpose: Medulloblastoma (MB) is the most common malignant brain tumor in children. About 30% MB isreleated to the abnormally activation of the Hedgehog signaling pathway. Smoothened(SMO) is a G protein-coupled receptor that interacts with the patched protein(PTCH) to transduce the hedgehog's proteins signal.This study analyzed the differential expression gene and obtained GO(Gene Ontology) terms and KEGG of these genes after SMO knockdown in Daoy medulloblastoma cells by transcriptome profiling (RNA-seq) .This study aims to provide the basis for subsequent study on medulloblastoma's driven genes. Methods: Cultured Daoy medulloblastoma cells were transfected with 50nM SMO small interference RNA(siRNA) or negtive control siRNA using Lipofectamine 2000 for 48 hours, and transfection efficiency was analyzed by reverse transcription polymerase chain reaction (qRT–PCR) and Western Blot. Then the transriptome profiles of siNC and siSMO cell were sequenced with high-throughput sequencing technology. Results: Using a standardized data analysis workflow, we mapped about 45 million sequence reads per sample. With comparative analysis of transcriptome of siNC and siSMO samples that each repeated three times, 216 differentially expressed genes (DEGs) were found, including 79 up-regulated and 137 down-regulated genes.Genes with q≤0.05 and |log2_ratio|≥1 are identified as DEGs. The ratio that sequence data mapping into reference genome is above 97%. Gene sequences were aligned to public datases such as GO, KEGG(kyoto Encyclopedia of Genes and Genomes) and STRING (Protein-Protein Interaction Networks Functional Enrichment Analysis). 47 genes were matched to GO database. 158 genes were up regulate in 114 pathways and 306 genes were down regulate in 179 pathways in KEGG database. Conclusions: In cancer research, cancer cell lines are important for examining and manipulating molecular and cellular process. DAOY cell line is grouped in the TP53 mutant SHH subgroup MB.Our study represents the first detailed analysis of SMO transcriptomes in Daoy medulloblastoma cells, with biologic replicates, generated by RNA-seq technology. We conclude that knockdown of SMO could participate in transcriptional regulation of many genes and lead to changes in many signaling pathways, witch provises important basis for further investigation of molecular mechanism in SHH subtype MS.
2020-03-31 | GSE147727 | GEO
Project description:Intervention type:DRUG
Name of intervention:Huaier
Dose form / Japanese Medical Device Nomenclature:GRANULES
Route of administration / Site of application:ORAL
Dose per administration:20?
g
Dosing frequency / Frequency of use:OTHER, SPECIFY
20g? per day
Planned duration of intervention:3 months to extending if necessary
Intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary
detailes of teratment arms:hepatocellular carcinoma, breast cancer, colorectal cancer and related gastrointestinal cancers, urologic cancers including prostate cancer, pancreas cancer, and lung cancer, etc.
Comparative intervention name:None
Dose form / Japanese Medical Device Nomenclature:
Route of administration / Site of application:
Dose per administration:
Dosing frequency / Frequency of use:
Planned duration of intervention:
Intended dose regimen:
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.
Study Design: Comparative test, None, No, open(masking not used), EXPLORATORY
| 98681 | ecrin-mdr-crc
Project description:OBJECTIVE: To investigate the differentially expressed genes related to the chemosensitivity of laryngeal squamous cell carcinoma ï¼LSCCï¼by microarrays arrays. METHODS: 1. A total number of 11 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (7 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis 2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened. RESULTS: 1. Analyzed by microarrays, there were 1554 genes significantly related to the sensitivity to chemotherapy; Among these 1554genes, 777 showed a higher expression in the tissue from patients who are sensitive to chemotherapy , while 785 presented the contrasting pattern. CONCLUSIONS: The research revealed a gene expression signature of chemosensitivity in laryngeal squamous cell carcinoma by microarrays arrays. The result will contribute to the understanding of the molecular basis of laryngeal squamous cell carcinoma and help to improve diagnosis and treatment. 1. A total number of 11 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (7 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis 2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened.
2016-08-16 | E-GEOD-85607 | biostudies-arrayexpress
Project description:This study aimed to explore the differential lncRNAs in CA and their probable function on CA development.We used RNA-sequencing to assess the genome-wide expression levels of lncRNAs in CA and paired adjacent normal tissues. We further validated the candidate lncRNAs in larger-size of CA specimen using RT-qPCR. Furthermore, the functional enrichment analysis for these candidate lncRNAs and differential mRNAs were analyzed using GO terms, KEGG and STRING database. The coexpressed mRNAs for the candidate lncRNAs, calculated by Pearson?s correlation coefficient, were also analyzed using GO analysis.A total of 657 lncRNAs and 1486 mRNAs were found to dysregulated in CA compared to adjacent mucosal tissues. The microarray data of candidate lncRNAs, including HOXC13-AS, HOTAIR, PICSAR, FGF14-AS1, ADGRD1-AS1, TMEM108-AS1, TUSC7 and FGF10-AS1, were validated with a larger-size of specimen using RT-qPCR. The functional GO term and pathways analysis of DEGs are associated with the pathogenesis and development of CA, including cell proliferation and development, cellular adhesion, immune defense, cell migration and chemotaxis, angiogenesis, and maintaining skin hemostasis.LncRNAs that were differentially expressed between CA and normal tissues may be helpful to explore effective recurrence risk markers and potential intervention targets for CA.
2024-04-25 | GSE172139 | GEO
Project description:This study aimed to explore the differential lncRNAs in CA and their probable function on CA development.We used RNA-sequencing to assess the genome-wide expression levels of lncRNAs in CA and paired adjacent normal tissues. We further validated the candidate lncRNAs in larger-size of CA specimen using RT-qPCR. Furthermore, the functional enrichment analysis for these candidate lncRNAs and differential mRNAs were analyzed using GO terms, KEGG and STRING database. The coexpressed mRNAs for the candidate lncRNAs, calculated by Pearson?s correlation coefficient, were also analyzed using GO analysis.A total of 657 lncRNAs and 1486 mRNAs were found to dysregulated in CA compared to adjacent mucosal tissues. The microarray data of candidate lncRNAs, including HOXC13-AS, HOTAIR, PICSAR, FGF14-AS1, ADGRD1-AS1, TMEM108-AS1, TUSC7 and FGF10-AS1, were validated with a larger-size of specimen using RT-qPCR. The functional GO term and pathways analysis of DEGs are associated with the pathogenesis and development of CA, including cell proliferation and development, cellular adhesion, immune defense, cell migration and chemotaxis, angiogenesis, and maintaining skin hemostasis.LncRNAs that were differentially expressed between CA and normal tissues may be helpful to explore effective recurrence risk markers and potential intervention targets for CA.
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2024-05-24 | PXD046592 | Pride