Fused inverse-normal method for integrated differential expression analysis of RNA-seq data

Use of next-generation sequencing technologies to transcriptomics (RNA-seq) for gene expression profiling has found widespread application in studying different biological conditions including cancers. However, RNA-seq experiments are still small sample size experiments due to the cost. Recently, an increased focus has been on meta-analysis methods for integrated differential expression analysis for exploration of potential biomarkers. In this study, we propose a p-value combination method for meta-analysis of multiple related RNA-seq studies that accounts for sample size of a study and direction of expression of genes in individual studies. The proposed method generalizes the inverse-normal method without increase in computational complexity and does not pre- or post-hoc filter genes that have conflicting direction of expression in different studies. Thus, the proposed method, as compared to the inverse-normal, has better potential for the discovery of differentially expressed genes (DEGs) with potentially conflicting differential signals from multiple studies related to disease. We demonstrated the use of the proposed method in detection of biologically relevant DEGs in glioblastoma (GBM), the most aggressive brain cancer. Our approach notably enabled the identification of over-expression in GBM compared to healthy controls of the oncogene RAD51, which has recently been shown to be a target for inhibition to enhance radiosensitivity of GBM cells during treatment. Pathway analysis identified multiple aberrant GBM related pathways as well as novel regulators such as TCF7L2 and MAPT as important upstream regulators in GBM. The proposed method provides a way to establish differential expression status for genes with conflicting direction of expression in individual RNA-seq studies. Hence, leading to further exploration of them as potential biomarkers for the disease

Additional file 1 of Fused inverse-normal method for integrated differential expression analysis of RNA-seq data

Additional file 1. Document contains interpretation of the fused inverse-normal (FIN) method, details of RNA-seq raw data processing using GALAXY, brief description of the simulation method, results of scenario 2 considered for meta-analysis and Ingenuity pathway analysis results

Additional file 1 of Fused inverse-normal method for integrated differential expression analysis of RNA-seq data

Additional file 1. Document contains interpretation of the fused inverse-normal (FIN) method, details of RNA-seq raw data processing using GALAXY, brief description of the simulation method, results of scenario 2 considered for meta-analysis and Ingenuity pathway analysis results

Mitotic DNA synthesis is caused by transcription-replication conflicts in BRCA2-deficient cells

Aberrant replication causes cells lacking BRCA2 to enter mitosis with under-replicated DNA, which activates a repair mechanism known as mitotic DNA synthesis (MiDAS). Here, we identify genome-wide the sites where MiDAS reactions occur when BRCA2 is abrogated. High-resolution profiling revealed that these sites are different from MiDAS at aphidicolin-induced common fragile sites in that they map to genomic regions replicating in the early S-phase, which are close to early-firing replication origins, are highly transcribed, and display R-loop-forming potential. Both transcription inhibition in early S-phase and RNaseH1 overexpression reduced MiDAS in BRCA2-deficient cells, indicating that transcription-replication conflicts (TRCs) and R-loops are the source of MiDAS. Importantly, the MiDAS sites identified in BRCA2-deficient cells also represent hotspots for genomic rearrangements in BRCA2-mutated breast tumors. Thus, our work provides a mechanism for how tumor-predisposing BRCA2 inactivation links transcription-induced DNA damage with mitotic DNA repair to fuel the genomic instability characteristic of cancer cells

Co-ordinated observations of VHF scintillations in India during February-March 1993

22-29The VHF scintillation observations made at a chain of stations in India during February-March 1993 under AICPITS (third campaign), using the 244 MHz radio beacon from FLEETSAT, and analysed jointly by all participating investigators at a workshop held at Raj kot are described. The occurrence features of scintillations during the third campaign were similar to those observed during the first campaign of March-April 1991. The maximum occurrence was, however, reduced to some extent due to the lower solar activity. The latitudinal variations showed an increased occurrence in the region of about 17-18o latitude. The data during the night of 19-20 Feb. 1993 when an extensive ‘Ionisation Hole Campaign’ was undertaken showed scintillations marked by earlier onset and longer duration at stations Waltair and Nuzvid than at the stat ions close to the magnetic equator. However, based on the average variations during February-March 1993 the onset at Tiruchendur, Anantpur and Walt air was at nearly the same time. The vertical rise velocity of the plasma depletions, estimated from the time delays in the onset of scintillations at latitudes away from the dip equator, was found to range from 40 m/s to 420 m/s in the altitude region 300-1350 km