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一文解鎖機制研究神器——IPA分析！

吉凱基因

2022.2.16

今天，我們一起看看IPA分析如何從組學數據中輕松get機制研究？

RNA-seq機制研究套餐采用了更高級的生信分析數據庫Ingenuity Pathway Analysis（IPA）來對測序數據進行分析，IPA所基于的后臺是一個高度結構化的ingenuity knowledge base數據庫，并且它是一個收費數據庫，每年的賬號使用費數十萬，該數據庫經歷20年的海量知識數據投入，號稱擁有近500名PhD對近700多種權威雜志進行全文閱讀，3000多種雜志進行摘要閱讀，保存每周更新一次。目前數據庫存儲了530萬條以上的生物實驗發(fā)現，150萬條互作信息和3萬種以上的分子信息；此外，還構建了完整的功能疾病分類數據庫，繪制了800種以上的信號通路，代謝通路等，為廣大科研工作者提供及時、準確的生物信息學數據支持。

吉凱基因IPA分析主要包含5個模塊

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一、經典通路分析

（尋找目的基因調控以后顯著影響的信號通路）

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二、上游調控分析

（尋找差異基因上游關鍵調控因子）

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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）? ?

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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）

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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系）

應用案例

案例一

技術路線：

細胞基因操+RNA-seq

?IPA分析

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后進行了RNA-Seq，利用IPA網絡分析模塊，分析了差異基因的重要調控網絡，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：

外周血單核細胞（PBMC)+RNA-seq

?IPA分析

Q-PCR驗證

總結：為了研究長期暴露于砷污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(fā)現：總共1,054個基因與尿砷水平的升高顯著相關其并且發(fā)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信號途徑）。

案例三

技術路線：

總結：該研究通過RNA-seq+IPA高級生信分析承上啟下，發(fā)現了TRIM24是GLUT4的主要下游調節(jié)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通過TRIM24-DDX58軸實現的。

案例四

技術路線：

總結：該研究通過RNA-seq+IPA高級生信分析承上啟下，發(fā)現了RAB3C促進結直腸癌發(fā)生發(fā)展的作用機制可能是通過調控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=23.239

2.Low-Molecular-Weight Protein Tyrosine Phosphatase Predicts Prostate Cancer Outcome by Increasing the Metastatic Potential ?IF=17.298

3. Global gene expression profiling in mouse plasma cell tumor precursor and bystander cells reveals potential intervention targets for plasma cell neoplasia IF=16.562

4. The pruritus- and TH2-associated cytokine IL-31 promotes growth of sensory nerves ?IF=14.11

5.Use of contraceptive depot medroxyprogesterone acetate is associated with impaired cervicovaginal mucosal integrity ?IF=12.28

6. Kidney-targeted inhibition of protein kinase C-a ameliorates nephrotoxic nephritis with restoration of mitochondrial dysfunction ?IF=8.306

7. LncRNA MIR31HG targets HIF1A and P21 to facilitate head and neck cancer cell proliferation and tumorigenesis by promoting cell-cycle progression ?IF=10.698

8. Secretory RAB GTPase 3C modulates IL6-STAT3 pathway to promote colon cancer metastasis and is associated with poor prognosis IF=10.698

9. Phosphorylation of αB-crystallin supports reactive astrogliosis in demyelination IF=9.58

10.In Vivo Therapeutic Success of MicroRNA-155 Antagomir in a Mouse Model of Lupus Alveolar Hemorrhage IF=9.02

11. An FGFR3 autocrine loop sustains acquired resistance to trastuzumab in gastric cancer patients IF=8.91

12.Glucose transporter 4 promotes head and neck squamous cell carcinoma metastasis through the TRIM24-DDX58 axis IF=8.731

13. Epigenetic modification of microRNA-200b contributes to diabetic vasculopathy IF=8.402

14.Identification of transcriptome signature for myocardial reductive stress? IF=7.79

15.Transcriptomic and Functional Analyses on the Effects of Dioxin on Insulin Secretion of Pancreatic Islets and #-cells ?IF=7.14

16. Human airway epithelial extracellular vesicle miRNA signature is altered upon asthma development ?IF=6.77

17.Essential role of JunD in cell proliferation is mediated via MYC signaling in prostate cancer cells ?IF=6.5

18.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=6.46

19. RGS4 maintains chronic pain symptoms in rodent models IF=6.07

20.PUM1 knockdown prevents tumor progression by activating the PERK/eIF2/ ATF4 signaling pathway in pancreatic adenocarcinoma cells IF=5.95

21. Lamin A/C negatively regulated by miR‐124‐3p modulates apoptosis of vascular smooth muscle cells during cyclic stretch application in rats ?IF=5.86

22.PBMC gene expression profiles of female Bangladeshi adults chronically exposed to arsenic-contaminated drinking water IF=5.714

23.Gene Expression Profiling of NFATc1-Knockdown in RAW 264.7 Cells: An Alternative Pathway for Macrophage Differentiation IF=5.656

24.Differential Regulation of TLE3 in Sertoli Cells of the Testes during Postnatal Development ?IF=5.656

25.Matcha green tea (MGT) inhibits the propagation of cancer stem cells (CSCs), by targeting mitochondrial metabolism, glycolysis and multiple cell signalling pathways IF=5.515

26.Long-term exercise prevents hepatic steatosis: a novel role of FABP1 in regulation of autophagy-lysosomal machinery? IF=5.39

27.Lysozyme-Induced Transcriptional Regulation of TNF-α Pathway Genes in Cells of the Monocyte Lineage IF=4.18

28.Moringa Isothiocyanate Activates Nrf2: Potential Role in Diabetic Nephropathy IF=3.545

29.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=2.933

30.Identification of the inhibitor of growth protein 4 (ING4) as a potential target in prostate cancer therapy IF=2.884