Dr.WL
今天，我們一起看看IPA分析如何從組學資料中輕鬆get機制研究？
RNA-seq機制研究套餐採用了更高階的生信分析資料庫Ingenuity Pathway Analysis（IPA）來對測序資料進行分析，IPA所基於的後臺是一個高度結構化的ingenuity knowledge base資料庫，並且它是一個收費資料庫，每年的賬號使用費數十萬，該資料庫經歷20年的海量知識資料投入，號稱擁有近500名PhD對近700多種權威雜誌進行全文閱讀，3000多種雜誌進行摘要閱讀，儲存每週更新一次。目前資料庫儲存了530萬條以上的生物實驗發現，150萬條互作資訊和3萬種以上的分子資訊；此外，還構建了完整的功能疾病分類資料庫，繪製了800種以上的訊號通路，代謝通路等，為廣大科研工作者提供及時、準確的生物資訊學資料支援。
IPA分析主要包含5個模組
“一、經典通路分析
（ 尋找目的基因調控以後顯著影響的訊號通路）
“二、上游調控分析
（尋找差異基因上游關鍵調控因子）
“三、疾病和功能分析
（尋找差異基因主要影響的疾病功能方向）
“四、調控效應分析
（尋找上游因子、差異基因、下游功能之間的可能作用途徑）
“五、互作網路分析
（尋找某一功能方向相關差異分子之間的互作關係）
應用案例
案例一
技術路線：
01
細胞基因操+RNA-seq
02
IPA分析
03
Q-PCR驗證
總結：為了探索生長蛋白4抑制劑（ING4）在前列腺癌（PC）中的作用機制，在LNCaP細胞中，敲低ING4後進行了RNA-Seq，利用IPA網路分析模組，分析了差異基因的重要調控網路，第一次從整個基因調控的層面展示了ING4對PC細胞的調控作用。
案例二
技術路線：
01
外周血單核細胞（PBMC)+RNA-seq
02
IPA分析
03
Q-PCR驗證
總結：為了研究長期暴露於砷汙染飲用水個體的基因表達變化；將29名受試者外周血單核細胞（PBMC）中提取的RNA進行RNA-seq檢測，IPA分析發現：總共1,054個基因與尿砷水平的升高顯著相關其並且發現了潛在的靶基因（DAPK1，EGR2，APP），microRNA（miR-155，-338，-210）以及與砷致癌相關的途徑（NOTCH訊號途徑）。
案例三
技術路線：
總結：該研究透過RNA-seq+IPA高階生信分析承上啟下，發現了TRIM24是GLUT4的主要下游調節子；證實DDX58是TRIM24的下游靶標，提示：GLUT4促進頭頸部鱗狀細胞癌轉移可能是透過TRIM24-DDX58軸實現的。
案例四
技術路線：
總結：該研究透過RNA-seq+IPA高階生信分析承上啟下，發現了RAB3C促進結直腸癌發生發展的作用機制可能是透過調控IL-6來實現的。
RNA-seq+IPA分析應用文獻集錦
1.Reperfusion-triggered stress protein response in the myocardium is blocked by post-conditioning. Systems biology pathway analysis highlights the key role of the canonical aryl-hydrocarbon receptor pathway IF=23.2392.Low-Molecular-Weight Protein Tyrosine Phosphatase Predicts Prostate Cancer Outcome by Increasing the Metastatic Potential IF=17.2983. Global gene expression profiling in mouse plasma cell tumor precursor and bystander cells reveals potential intervention targets for plasma cell neoplasia IF=16.5624. The pruritus- and TH2-associated cytokine IL-31 promotes growth of sensory nerves IF=14.115.Use of contraceptive depot medroxyprogesterone acetate is associated with impaired cervicovaginal mucosal integrity IF=12.286. Kidney-targeted inhibition of protein kinase C-a ameliorates nephrotoxic nephritis with restoration of mitochondrial dysfunction IF=8.3067. LncRNA MIR31HG targets HIF1A and P21 to facilitate head and neck cancer cell proliferation and tumorigenesis by promoting cell-cycle progression IF=10.6988. Secretory RAB GTPase 3C modulates IL6-STAT3 pathway to promote colon cancer metastasis and is associated with poor prognosis IF=10.6989. Phosphorylation of αB-crystallin supports reactive astrogliosis in demyelination IF=9.5810.In Vivo Therapeutic Success of MicroRNA-155 Antagomir in a Mouse Model of Lupus Alveolar Hemorrhage IF=9.0211. An FGFR3 autocrine loop sustains acquired resistance to trastuzumab in gastric cancer patients IF=8.9112.Glucose transporter 4 promotes head and neck squamous cell carcinoma metastasis through the TRIM24-DDX58 axis IF=8.73113. Epigenetic modification of microRNA-200b contributes to diabetic vasculopathy IF=8.40214.Identification of transcriptome signature for myocardial reductive stress IF=7.7915.Transcriptomic and Functional Analyses on the Effects of Dioxin on Insulin Secretion of Pancreatic Islets and #-cells IF=7.1416. Human airway epithelial extracellular vesicle miRNA signature is altered upon asthma development IF=6.7717.Essential role of JunD in cell proliferation is mediated via MYC signaling in prostate cancer cells IF=6.518.Poly(ADP-ribose) polymerase 1 is necessary for coactivating hypoxia-inducible factor-1- dependent gene expression by Epstein-Barr virus latent membrane protein 1 IF=6.4619. RGS4 maintains chronic pain symptoms in rodent models IF=6.0720.PUM1 knockdown prevents tumor progression by activating the PERK/eIF2/ ATF4 signaling pathway in pancreatic adenocarcinoma cells IF=5.9521. Lamin A/C negatively regulated by miR‐124‐3p modulates apoptosis of vascular smooth muscle cells during cyclic stretch application in rats IF=5.8622.PBMC gene expression profiles of female Bangladeshi adults chronically exposed to arsenic-contaminated drinking water IF=5.71423.Gene Expression Profiling of NFATc1-Knockdown in RAW 264.7 Cells: An Alternative Pathway for Macrophage Differentiation IF=5.65624.Differential Regulation of TLE3 in Sertoli Cells of the Testes during Postnatal Development IF=5.65625.Matcha green tea (MGT) inhibits the propagation of cancer stem cells (CSCs), by targeting mitochondrial metabolism, glycolysis and multiple cell signalling pathways IF=5.51526.Long-term exercise prevents hepatic steatosis: a novel role of FABP1 in regulation of autophagy-lysosomal machinery IF=5.3927.Lysozyme-Induced Transcriptional Regulation of TNF-α Pathway Genes in Cells of the Monocyte Lineage IF=4.1828.Moringa Isothiocyanate Activates Nrf2: Potential Role in Diabetic Nephropathy IF=3.54529.IL-1-conferred gene expression pattern in ERα+ BCa and AR+ PCa cells is intrinsic to ERα− BCa and AR− PCa cells and promotes cell survival IF=2.93330.Identification of the inhibitor of growth protein 4 (ING4) as a potential target in prostate cancer therapy IF=2.884
