Dataset Information

MCU interactome from mitochondria proteome

ABSTRACT: The interactome of MCU was determined by AP-MS in a minaturised approach. This dataset was the test dataset to demonstrate the robustness of the method.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Shane Austin

LAB HEAD: Karin Nowikovsky

PROVIDER: PXD029646 | Pride | 2022-06-23

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	M546-E01-CAB6-P7621-1.dat	Other
	M546-E01-CAB6-P7621-1.mgf	Mgf
	M546-E01-CAB6-P7621-1.pidres.xml	Xml
	M546-E01-CAB6-P7621-1.raw	Raw
	M546-E02-CAB6-P7622-1.dat	Other

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Project description:The purpose of our study was to construct prostate cancer cell-specific interactome by aggregating microarray samples available in public, and identify novel transcriptional regulators that control prostate cancer cell cycle progression. We collected 121 samples of PC-3 cell microarray data from 11 prior studies and our own study data, GSE45567, and performed pre-processing steps, such as quality control test, normalization, and batch effect adjusting. In quality control test, 10 low-quality samples were removed. The matrix data we deposited in GEO has normalized log2 signal intensity of 11,877 genes common in 110 samples, as the 110 samples came from different Affymetrix. The Gene IDs were identified by Entrez Gene IDs that overlapped across different Affymetrix platforms (File: GSE67157_Matrix_PC-3cell_Interactome.txt). In GSE45567 dataset, which is one of the 12 data sets, we selected microarray samples of vehicle-, cineol-, linalool-, and geraniol-treated PC-3 cells, and performed unsupervised clustering analysis to establish dependable clusters of a clear phenotypic transition. Then, the gene set specifically enriched or depleted in the geraniol cluster against vehicle cluster was used for gene set enrichment analysis (GSEA). We found cell cycle-related gene signatures were specifically down-regulated in the geraniol cluster. PC-3 cell-specific interactome was assembled from 110 microarray samples by Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe, PMID: 16723010). We used Master Regulator Analysis-Fisher’s Extact Test (MRA-FET, PMID: 20531406) to infer transcription factors which are geraniol target molecules and control cell cycle gene signatures. We discovered E2F8 is as a master regulator to modulate geraniol-specific genes toward G2/M cell cycle arrest. Our findings will provide biological insights into the role of E2F8 in prostate cancer for transcriptional regulation leading to the development of cell cycle-targeting chemotherapeutic reagent. In addition, our approach serves as an example to decide the most potent anti-cancer regime in other cancer types and identify the target molecules of cancer-preventive reagents through computational analyses.

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MCU interactome from mitochondria proteome

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