1 项目概述

项目编号GDMR21010245_sup_6
样品信息LL-1¦LL-2¦LL-3¦LN-1¦LN-2¦LN-3
TL-1¦TL-2¦TL-3¦TN-1¦TN-2¦TN-3
分组方案LL :LL-1&LL-2&LL-3¦LN :LN-1&LN-2&LN-3¦TL :TL-1&TL-2&TL-3¦TN :TN-1&TN-2&TN-3
两组差异分析方案LN-vs-LL¦TN-vs-TL¦LL-vs-TL¦LN-vs-TN

2 项目简介

2.1 背景介绍

由转录组和代谢组数据获得了样本在基因表达水平和代谢物水平的差异特征。然而生物系统中转录与代谢并不是独立发生的，为揭示基因表达与代谢物之间的调控影响机制，可基于“参与同一生物过程的基因或代谢物具有相同或相似的变化规律”进行二者的关联分析。

为筛选获得对样本分组有影响的关联基因与代谢物集合，分析关联特征，基于基因表达量和代谢物丰度两组数据进行3种模型分析：1）Pathway功能模型，查询基因与代谢物共有的KEGG 代谢通路（pathway），分析共有pathway中基因与代谢物的关联特征；2）O2PLS（Bidirectional orthogonal projections to latent structures)模型，使用基因表达量与代谢物丰度数据构建 O2PLS模型，通过模型预测，获得有关联性的基因与代谢物集合并分析；3）相关性系数模型（当样本分组 ≥ 3时，进行此模型分析），计算基因表达量与代谢物丰度的pearson相关性系数，并以热图和网络图展示。

Fig 2-1-1 信息分析流程图

广州基迪奥生物科技有限公司



3 Pathway功能模型

3.1 共有代谢通路分析

通过组间差异分析，由转录组数据获得了差异表达的基因，由代谢组数据获得了差异表达的代谢物，并进行了各自组学的KEGG富集分析。在关联分析中，将针对基因与代谢物进行共有KEGG pathway的分析[1][2][3]。包含三种类型：

具体分析结果如下：

Tab 3-1-1 共有 pathway 统计
关联类型 基因数据来源 代谢物数据来源 共有pathway Pathway 注释表
差异基因与差异代谢物LN-vs-LL LN-vs-LL LN-vs-LL.htm LN-vs-LL.path.xls
TN-vs-TL TN-vs-TL TN-vs-TL.htm TN-vs-TL.path.xls
LL-vs-TL LL-vs-TL LL-vs-TL.htm LL-vs-TL.path.xls
LN-vs-TN LN-vs-TN LN-vs-TN.htm LN-vs-TN.path.xls
差异基因与所有代谢物LN-vs-LL all LN-vs-LL_all.htm LN-vs-LL_all.path.xls
TN-vs-TL all TN-vs-TL_all.htm TN-vs-TL_all.path.xls
LL-vs-TL all LL-vs-TL_all.htm LL-vs-TL_all.path.xls
LN-vs-TN all LN-vs-TN_all.htm LN-vs-TN_all.path.xls
所有基因与所有代谢物 all all all.htm all.path.xls
3.2 Pathway map

点击共有pathway分析页面的KEGG描述，可链接基因与代谢物相关联的pathway map，示例如下：

Fig 3-2-1 差异代谢物与差异基因关联示例

广州基迪奥生物科技有限公司



4 O2PLS模型分析

基于所有转录组和所有代谢组数据，我们利用OmicsPLS包开展O2PLS分析[4]。O2PLS模型适用于两个组学数据的关联分析，可在两个数据矩阵中进行双向建模和预测。O2PLS模型通过计算，将每个组学的数据都分解为三个部分，即关联部分（joint part，即与另一组学关联程度很大的部分）、正交部分（Systematic/Orthogonal part，即只对本组学数据有影响、而对另一组学数据没有影响的部分）、噪音部分（noise part，即对两组学数据都没有影响的部分），如下图所示。各部分对总变异的解释程度以R2表示，值越高表示模型的解释能力越好。模型的过拟合和不足都会降低R2。

Fig 4-0-1 o2pls模型示例

OmicPLS包进行O2PLS模型分析的步骤如下：

1）对两个独立数据集（X，Y，如基因表达量和代谢物丰度数据）分别进行标准化，使总平方和为1，以消除组学数据数量级差异的影响，使统计分析更科学。

2）Cross-validation：确定组分个数。以关联部分组分个数a大于1，基因正交部分组分个数ax和代谢组正交部分组分个数ay大于0开始，进行多次不同数值组合的预建模，计算预测误差。

3）Fitting：最适建模。选取预测误差最小时，对应的组分个数n，nx，ny来构建最适模型。

4）输出各部分贡献度（R2），绘制载荷图。

4.1 模型构建

由于模型的拟合不足或过拟合都会对数据分析造成影响，因此在建立模型之前，我们会对模型进行预评估。模型的关联和正交部分包含一定数量的组分（component，类似PCA分析的主成分PC1、PC2）。我们采用交叉验证法（cross-validation）对每部分所包含的组分个数进行评估与设定。交叉验证法通过多次预建模，选择预测误差（prediction error）最小的模型进行后续分析。

Tab 4-1-1 O2PLS模型参数及预测误差值
Modelnxnynprediction error
dif0140.8159481
LN-vs-LL0040.8718620
TN-vs-TL0040.7448241
LL-vs-TL0030.9848046
LN-vs-TN0040.5221112

4.2 贡献度评估

贡献度是指模型各部分对总变异的解释程度，用R2表示。R2值越高，表示该部分对模型的解释能力越好。

Tab 4-2-1 O2PLS模型各部分组成情况
ModelR2XR2YR2XcorrR2Ycorr
dif0.9110.9470.9110.941
LN-vs-LL0.9780.9880.9780.988
TN-vs-TL0.9780.9870.9780.987
LL-vs-TL0.9340.9810.9340.981
LN-vs-TN0.9910.9930.9910.993

4.3 载荷图

为了查看哪些代谢物和基因相互关联，我们对joint部分的变量分别绘制不同组学的载荷图（loadings plot）。载荷值（loading value）表示变量（代谢物/基因）在各组分的解释能力（即对组间差异的贡献度），载荷值的正负表示与另一组学正关联或负相关；载荷值的绝对值越大，表示关联越强。

  • dif
  • LN-vs-LL
  • TN-vs-TL
  • LL-vs-TL
  • LN-vs-TN

Fig 4-3-1 两组学O2PLS载荷图


4.4 组间元素关联分析

根据元素loading值结果，我们筛选出前两个维度loading值平方和前25的基因和代谢物进行整合绘制loading图，以展示关联程度最大的基因和代谢物。

差异代谢物与差异基因（dif）O2PLS分析loading值结果如下：

Tab 4-4-1 代谢组数据的loading分值表
MetaboliteLoading_1Loading_2MS2_nameMS1_nameformulartminmzClassCASHMDBC_IDPathwayKEGG_B_classKEGG_A_class
Com_4230_pos-0.1132438606220710.09424621805586742-morpholinophenyl 3,5-dimethyl-4-isoxazolesulfonate--C15 H18 N2 O5 S6.476339.10037----------
Com_471_pos0.139021309893661-0.046495213512659Gly-Tyr--C11 H14 N2 O43.322239.10249Carboxylic acids and derivatives658-79-7HMDB0028853----
Com_871_neg-0.08942034094714320.11161575990723N-(1,2,3,4-tetrahydro-1-naphthalenyl)benzenesulfonamide--C16 H17 N O2 S2.684286.09299----------
Com_1241_pos-0.09842744113115280.102953405130596YMH--C20 H27 N5 O5 S9.536472.15707----------
Com_43_neg-0.0417432491290720.133817469512239Phenylacetylglycine--C10 H11 N O37.014192.06671Carboxylic acids and derivatives500-98-1HMDB0000821C05598ko00360//Phenylalanine metabolismAmino acid metabolismMetabolism
Com_2189_pos-0.09099760523706580.106458156729543-Hydroxyalprazolam--C17 H13 Cl N4 O8.957325.08807----------
Com_69_neg-0.100682763421230.09658402106037Oxoamide--C10 H12 N2 O28.805191.08255Organooxygen compounds713-05-3HMDB0001004----
Com_100_pos-0.08324373032182060.111855671470694trans-3-Hydroxycotinine--C10 H12 N2 O29.989193.09712Pyridines and derivatives34834-67-8HMDB0001390----
Com_99_pos-0.0827898470585250.112164913550825Indole-3-acetic acid--C10 H9 N O29.947176.07037Indoles and derivatives87-51-4HMDB0000197C00954ko01100//Metabolic pathways;ko00380//Tryptophan metabolismAmino acid metabolism;Global and overview mapsMetabolism
Com_410_pos-0.1153908347049680.07590828097821441-Phenyl-3-methyl-5-pyrazolone--C10 H10 N2 O8.711175.0865Azoles89-25-8HMDB0006240----
Com_254_pos-0.09663689042642110.0970809007908701Pectolinarin--C29 H34 O1511.994623.19794----------
Com_3450_pos-0.0921781941553330.1011055252460112-(4-methoxyphenyl)-3-(2-phenyl-1H-imidazol-4-yl)acrylonitrile--C19 H15 N3 O11.019302.12579----------
Com_1315_pos-0.1088528386958840.0827923828388198WLK--C23 H35 N5 O46.568428.26154----------
Com_4489_pos-0.1006497491624750.09219872735176461-(4-methylphenyl)-3,5-diphenylpent-2-ene-1,5-dione--C24 H20 O212.449363.13657----------
Com_3927_pos0.0770228709739155-0.11246197351702Sulfamethazine--C12 H14 N4 O2 S12.089279.09302Benzene and substituted derivatives57-68-1HMDB0015522----
Com_1685_pos-0.1032094995677010.0883841028425779--3-MethylindoleC9 H9 N8.674132.08076Indoles and derivatives83-34-1HMDB0000466----
Com_2489_pos-0.04155594267134970.12936676687919Cytidine--C9 H13 N3 O51.518244.09261Pyrimidine nucleosides65-46-3HMDB0000089C00475ko01100//Metabolic pathways;ko00240//Pyrimidine metabolismGlobal and overview maps;Nucleotide metabolismMetabolism
Com_2463_pos-0.09440763203947170.09642030821499862-Isopropylmalic acid--C7 H12 O51.356194.10226Fatty Acyls3237-44-3HMDB0000402C02504ko01100//Metabolic pathways;ko01110//Biosynthesis of secondary metabolites;ko01230//Biosynthesis of amino acids;ko01210//2-Oxocarboxylic acid metabolism;ko00620//Pyruvate metabolism;ko00290//Valine, leucine and isoleucine biosynthesisAmino acid metabolism;Carbohydrate metabolism;Global and overview mapsMetabolism
Com_1603_neg0.03453504293231790.129247748973283Guanosine-3',5'-cyclic monophosphate--C10 H12 N5 O7 P2.056344.03339----------
Com_511_pos0.09230903282620650.09415304429203126-(3-hydroxybutan-2-yl)-5-(hydroxymethyl)-4-methoxy-2H-pyran-2-one--C11 H16 O52.308267.05841----------
Com_429_pos0.0151211687906818-0.13044200192806DL-Arginine--C6 H14 N4 O21.351175.11885----------
Com_2878_pos-0.00248748912616449-0.130862673867085HexCer-NS (d18:1/16:0)--C40 H77 N O816.646700.57056----------
Com_3609_pos0.0246237824160437-0.128473003107808Amoxicillin--C16 H19 N3 O5 S6.032388.09918Lactams26787-78-0HMDB0015193----
Com_303_pos-0.04194416149553910.122586267497989L-Glutathione oxidized--C20 H32 N6 O12 S22.218613.1582----------
Com_53_neg0.07978925668184950.10136901610249Uridine--C9 H12 N2 O62.369243.06209Pyrimidine nucleosides58-96-8HMDB0000296C00299ko01100//Metabolic pathways;ko00240//Pyrimidine metabolismGlobal and overview maps;Nucleotide metabolismMetabolism

Tab 4-4-2 转录组数据的loading分值表
TranscriptLoading_1Loading_2SymbolDescriptionKEGG_A_classKEGG_B_classPathwayK_IDGO.ComponentGO.FunctionGO.Process
ncbi_100510947-0.0254054008430117-0.0531052391889094PTGDR2prostaglandin D2 receptor 2, transcript variant X1----GO:0005887//integral component of plasma membrane;GO:0016020//membrane;GO:0016021//integral component of membrane;GO:0043005//neuron projectionGO:0001785//prostaglandin J receptor activity;GO:0004930//G protein-coupled receptor activity;GO:0004956//prostaglandin D receptor activity;GO:0004958//prostaglandin F receptor activity;GO:0042277//peptide binding;GO:0042923//neuropeptide bindingGO:0006935//chemotaxis;GO:0007165//signal transduction;GO:0007186//G protein-coupled receptor signaling pathway;GO:0007193//adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;GO:0007218//neuropeptide signaling pathway;GO:0019722//calcium-mediated signaling;GO:0045745//positive regulation of G protein-coupled receptor signaling pathway;GO:2000255//negative regulation of male germ cell proliferation
ncbi_100737053-0.016857417820817-0.0555806709745357PPP2R2Cprotein phosphatase 2 regulatory subunit Bgamma, transcript variant X1Environmental Information Processing;Human Diseases;Cellular Processes;Environmental Information Processing;Organismal Systems;Organismal Systems;Human Diseases;Environmental Information Processing;Environmental Information Processing;Human Diseases;Genetic Information ProcessingSignal transduction;Infectious diseases;Cellular community - eukaryotes;Signal transduction;Circulatory system;Nervous system;Infectious diseases;Signal transduction;Signal transduction;Infectious diseases;Translationko04151//PI3K-Akt signaling pathway;ko05165//Human papillomavirus infection;ko04530//Tight junction;ko04390//Hippo signaling pathway;ko04261//Adrenergic signaling in cardiomyocytes;ko04728//Dopaminergic synapse;ko05160//Hepatitis C;ko04152//AMPK signaling pathway;ko04071//Sphingolipid signaling pathway;ko05142//Chagas disease (American trypanosomiasis);ko03015//mRNA surveillance pathwayK04354;K04354;K04354;K04354;K04354;K04354;K04354;K04354;K04354;K04354;K04354GO:0000159//protein phosphatase type 2A complex;GO:0005829//cytosolGO:0005515//protein binding;GO:0019888//protein phosphatase regulator activityGO:0043666//regulation of phosphoprotein phosphatase activity;GO:0070262//peptidyl-serine dephosphorylation
ncbi_397417-0.0180761366834718-0.0550187975414674MT1Ametallothionein 1AOrganismal SystemsDigestive systemko04978//Mineral absorptionK14739GO:0005623//cell;GO:0005634//nucleus;GO:0005737//cytoplasm;GO:0048471//perinuclear region of cytoplasmGO:0008270//zinc ion binding;GO:0046872//metal ion bindingGO:0006882//cellular zinc ion homeostasis;GO:0010273//detoxification of copper ion;GO:0045926//negative regulation of growth;GO:0071276//cellular response to cadmium ion;GO:0071280//cellular response to copper ion;GO:0071294//cellular response to zinc ion
ncbi_100621654-0.0238966663605797-0.0526935463245403FAM3Dfamily with sequence similarity 3 member D, transcript variant X12----GO:0016020//membrane;GO:0016021//integral component of membrane-GO:0070093//negative regulation of glucagon secretion
ncbi_397195-0.0279972181885951-0.0505241165969217ADMadrenomedullin----GO:0005576//extracellular region;GO:0005615//extracellular space;GO:0005737//cytoplasmGO:0005179//hormone activity;GO:0031700//adrenomedullin receptor bindingGO:0001570//vasculogenesis;GO:0001843//neural tube closure;GO:0002031//G protein-coupled receptor internalization;GO:0003073//regulation of systemic arterial blood pressure;GO:0007189//adenylate cyclase-activating G protein-coupled receptor signaling pathway;GO:0007507//heart development;GO:0008284//positive regulation of cell proliferation;GO:0010460//positive regulation of heart rate;GO:0031623//receptor internalization;GO:0035809//regulation of urine volume;GO:0043116//negative regulation of vascular permeability;GO:0045766//positive regulation of angiogenesis;GO:0045906//negative regulation of vasoconstriction;GO:0048589//developmental growth;GO:0060670//branching involved in labyrinthine layer morphogenesis;GO:0060712//spongiotrophoblast layer development;GO:0097084//vascular smooth muscle cell development;GO:0097647//amylin receptor signaling pathway;GO:1990410//adrenomedullin receptor signaling pathway;GO:2001214//positive regulation of vasculogenesis
ncbi_100515346-0.0172857975324992-0.0550023250887469ACKR3atypical chemokine receptor 3Environmental Information ProcessingSignaling molecules and interactionko04060//Cytokine-cytokine receptor interactionK04304GO:0005623//cell;GO:0005768//endosome;GO:0005886//plasma membrane;GO:0005905//clathrin-coated pit;GO:0009897//external side of plasma membrane;GO:0009986//cell surface;GO:0016020//membrane;GO:0016021//integral component of membrane;GO:0043231//intracellular membrane-bounded organelleGO:0004930//G protein-coupled receptor activity;GO:0005044//scavenger receptor activity;GO:0015026//coreceptor activity;GO:0016493//C-C chemokine receptor activity;GO:0016494//C-X-C chemokine receptor activity;GO:0019956//chemokine binding;GO:0019957//C-C chemokine binding;GO:0019958//C-X-C chemokine bindingGO:0001525//angiogenesis;GO:0001570//vasculogenesis;GO:0006935//chemotaxis;GO:0006955//immune response;GO:0007165//signal transduction;GO:0007186//G protein-coupled receptor signaling pathway;GO:0007204//positive regulation of cytosolic calcium ion concentration;GO:0019722//calcium-mediated signaling;GO:0031623//receptor internalization;GO:0060326//cell chemotaxis;GO:0070098//chemokine-mediated signaling pathway;GO:0070374//positive regulation of ERK1 and ERK2 cascade;GO:1902230//negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
ncbi_100154178-0.011605704099471-0.0562984310812665NEDD9neural precursor cell expressed, developmentally down-regulated 9, transcript variant X1----GO:0000922//spindle pole;GO:0005634//nucleus;GO:0005654//nucleoplasm;GO:0005737//cytoplasm;GO:0005829//cytosol;GO:0005886//plasma membraneGO:0005515//protein binding;GO:1990782//protein tyrosine kinase bindingGO:0007169//transmembrane receptor protein tyrosine kinase signaling pathway;GO:0016477//cell migration;GO:0030335//positive regulation of cell migration;GO:0061098//positive regulation of protein tyrosine kinase activity;GO:0090527//actin filament reorganization;GO:0090630//activation of GTPase activity;GO:1900026//positive regulation of substrate adhesion-dependent cell spreading
ncbi_102158732-0.01499091685618-0.0553190782599183FXYD6FXYD domain containing ion transport regulator 6, transcript variant X1----GO:0016020//membrane;GO:0016021//integral component of membraneGO:0017080//sodium channel regulator activity;GO:0099106//ion channel regulator activityGO:0006811//ion transport;GO:0043269//regulation of ion transport;GO:2000649//regulation of sodium ion transmembrane transporter activity
ncbi_102163819-0.0167653255151326-0.054730658028349MS4A10membrane spanning 4-domains A10, transcript variant X1----GO:0016020//membrane;GO:0016021//integral component of membrane--
ncbi_397115-0.0123182989734467-0.05586759958117ARG1arginase 1Metabolism;Human Diseases;Metabolism;Metabolism;MetabolismGlobal and overview maps;Infectious diseases;Global and overview maps;Amino acid metabolism;Amino acid metabolismko01100//Metabolic pathways;ko05146//Amoebiasis;ko01230//Biosynthesis of amino acids;ko00330//Arginine and proline metabolism;ko00220//Arginine biosynthesisK01476;K01476;K01476;K01476;K01476GO:0005615//extracellular space;GO:0005737//cytoplasm;GO:0005829//cytosolGO:0004053//arginase activity;GO:0016787//hydrolase activity;GO:0016813//hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines;GO:0030145//manganese ion binding;GO:0046872//metal ion bindingGO:0000050//urea cycle;GO:0006525//arginine metabolic process;GO:0019547//arginine catabolic process to ornithine;GO:0042130//negative regulation of T cell proliferation;GO:0042832//defense response to protozoan;GO:0046007//negative regulation of activated T cell proliferation;GO:0060336//negative regulation of interferon-gamma-mediated signaling pathway;GO:0070965//positive regulation of neutrophil mediated killing of fungus;GO:2000552//negative regulation of T-helper 2 cell cytokine production
ncbi_100519355-0.0137648035256135-0.0554794719196159F2RL2coagulation factor II thrombin receptor like 2Environmental Information Processing;Organismal SystemsSignaling molecules and interaction;Immune systemko04080//Neuroactive ligand-receptor interaction;ko04610//Complement and coagulation cascadesK04235;K04235GO:0005623//cell;GO:0005887//integral component of plasma membrane;GO:0016020//membrane;GO:0016021//integral component of membrane;GO:0016324//apical plasma membrane;GO:0032991//protein-containing complexGO:0004930//G protein-coupled receptor activity;GO:0015057//thrombin-activated receptor activityGO:0007165//signal transduction;GO:0007186//G protein-coupled receptor signaling pathway;GO:0007596//blood coagulation;GO:0035025//positive regulation of Rho protein signal transduction;GO:0051482//positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway;GO:0070493//thrombin-activated receptor signaling pathway
ncbi_100620701-0.0135341005622964-0.0554949909155963ECM1extracellular matrix protein 1, transcript variant X1----GO:0005576//extracellular region;GO:0005615//extracellular space;GO:0062023//collagen-containing extracellular matrixGO:0002020//protease binding;GO:0005134//interleukin-2 receptor binding;GO:0008022//protein C-terminus binding;GO:0019899//enzyme binding;GO:0043236//laminin bindingGO:0001938//positive regulation of endothelial cell proliferation;GO:0001960//negative regulation of cytokine-mediated signaling pathway;GO:0002063//chondrocyte development;GO:0002828//regulation of type 2 immune response;GO:0003416//endochondral bone growth;GO:0006357//regulation of transcription by RNA polymerase II;GO:0006954//inflammatory response;GO:0007165//signal transduction;GO:0010466//negative regulation of peptidase activity;GO:0030500//regulation of bone mineralization;GO:0030502//negative regulation of bone mineralization;GO:0045766//positive regulation of angiogenesis;GO:2000404//regulation of T cell migration
ncbi_100157572-0.0188364773680572-0.053791734918358GALNT15polypeptide N-acetylgalactosaminyltransferase 15Metabolism;MetabolismGlobal and overview maps;Glycan biosynthesis and metabolismko01100//Metabolic pathways;ko00512//Mucin type O-glycan biosynthesisK00710;K00710GO:0000139//Golgi membrane;GO:0005794//Golgi apparatus;GO:0016020//membrane;GO:0016021//integral component of membrane;GO:0030133//transport vesicleGO:0016740//transferase activity;GO:0016757//transferase activity, transferring glycosyl groups;GO:0030246//carbohydrate bindingGO:0006486//protein glycosylation
ncbi_1001444900.02276144423597460.0519151399685711IGFBP4insulin like growth factor binding protein 4----GO:0005576//extracellular region;GO:0005615//extracellular spaceGO:0005520//insulin-like growth factor binding;GO:0031994//insulin-like growth factor I binding;GO:0031995//insulin-like growth factor II bindingGO:0001558//regulation of cell growth;GO:0010906//regulation of glucose metabolic process;GO:0040008//regulation of growth;GO:0043410//positive regulation of MAPK cascade;GO:0043567//regulation of insulin-like growth factor receptor signaling pathway;GO:0043568//positive regulation of insulin-like growth factor receptor signaling pathway;GO:0044342//type B pancreatic cell proliferation
ncbi_106509958-0.0114308285536688-0.0554470744577443MTSS1MTSS1, I-BAR domain containing, transcript variant X1-----GO:0003779//actin bindingGO:0007009//plasma membrane organization;GO:0030036//actin cytoskeleton organization
ncbi_397566-0.0183189818211-0.0534487530012847PGM1phosphoglucomutase 1Metabolism;Metabolism;Metabolism;Metabolism;Metabolism;Metabolism;MetabolismGlobal and overview maps;Nucleotide metabolism;Carbohydrate metabolism;Carbohydrate metabolism;Carbohydrate metabolism;Carbohydrate metabolism;Carbohydrate metabolismko01100//Metabolic pathways;ko00230//Purine metabolism;ko00010//Glycolysis / Gluconeogenesis;ko00520//Amino sugar and nucleotide sugar metabolism;ko00500//Starch and sucrose metabolism;ko00052//Galactose metabolism;ko00030//Pentose phosphate pathwayK01835;K01835;K01835;K01835;K01835;K01835;K01835GO:0005829//cytosolGO:0000287//magnesium ion binding;GO:0004614//phosphoglucomutase activity;GO:0016868//intramolecular transferase activity, phosphotransferases;GO:0046872//metal ion bindingGO:0005975//carbohydrate metabolic process;GO:0005978//glycogen biosynthetic process;GO:0006006//glucose metabolic process;GO:0019388//galactose catabolic process;GO:0071704//organic substance metabolic process
ncbi_106510284-0.0216268779395072-0.0521847908039349LOC106510284apolipoprotein L3-like, transcript variant X1----GO:0005576//extracellular region;GO:0005615//extracellular space;GO:0016020//membrane;GO:0016021//integral component of membraneGO:0008289//lipid bindingGO:0006869//lipid transport;GO:0042157//lipoprotein metabolic process
ncbi_100154641-0.010827812970905-0.0552417969605562ABI3BPABI family member 3 binding protein, transcript variant X1-----GO:0005515//protein binding-
ncbi_100157437-0.0121755678428262-0.0548716626985484RGS4regulator of G protein signaling 4----GO:0005634//nucleus;GO:0005737//cytoplasmGO:0005096//GTPase activator activityGO:0007186//G protein-coupled receptor signaling pathway;GO:0043547//positive regulation of GTPase activity
ncbi_100525009-0.0170287176448306-0.0535474025446255ZNF395zinc finger protein 395, transcript variant 1----GO:0005634//nucleus;GO:0005654//nucleoplasm;GO:0005737//cytoplasm;GO:0005829//cytosolGO:0000978//RNA polymerase II proximal promoter sequence-specific DNA binding;GO:0000987//proximal promoter sequence-specific DNA binding;GO:0003676//nucleic acid binding;GO:0003677//DNA binding;GO:0005515//protein bindingGO:0006357//regulation of transcription by RNA polymerase II
ncbi_102162371-0.0128564723912642-0.0546035831341483FBLN7fibulin 7-----GO:0005509//calcium ion binding-
ncbi_396775-0.00875354792375368-0.0553816386529524TIMP3TIMP metallopeptidase inhibitor 3Human Diseases;Human DiseasesCancers;Cancersko05205//Proteoglycans in cancer;ko05206//MicroRNAs in cancerK16866;K16866GO:0005576//extracellular region;GO:0005604//basement membrane;GO:0005615//extracellular space;GO:0031012//extracellular matrixGO:0002020//protease binding;GO:0005515//protein binding;GO:0008191//metalloendopeptidase inhibitor activityGO:0009725//response to hormone;GO:0010033//response to organic substance;GO:0010951//negative regulation of endopeptidase activity;GO:0034097//response to cytokine;GO:0051045//negative regulation of membrane protein ectodomain proteolysis;GO:0070373//negative regulation of ERK1 and ERK2 cascade;GO:0071310//cellular response to organic substance;GO:1903984//positive regulation of TRAIL-activated apoptotic signaling pathway;GO:1904684//negative regulation of metalloendopeptidase activity
ncbi_396877-0.0237446042805543-0.0505703311769263CFDcomplement factor DOrganismal Systems;Human DiseasesImmune system;Infectious diseasesko04610//Complement and coagulation cascades;ko05150//Staphylococcus aureus infectionK01334;K01334GO:0005576//extracellular region;GO:0005615//extracellular spaceGO:0004252//serine-type endopeptidase activity;GO:0008233//peptidase activity;GO:0008236//serine-type peptidase activity;GO:0016787//hydrolase activityGO:0002376//immune system process;GO:0006508//proteolysis;GO:0006957//complement activation, alternative pathway;GO:0007219//Notch signaling pathway;GO:0009617//response to bacterium;GO:0045087//innate immune response
ncbi_100153407-0.0177987465719213-0.0529327073648918CSDC2cold shock domain containing C2----GO:0005737//cytoplasmGO:0003676//nucleic acid binding;GO:0003730//mRNA 3'-UTR bindingGO:0043488//regulation of mRNA stability
ncbi_396670-0.00840727947082502-0.0551246758201098SCDstearoyl-CoA desaturaseEnvironmental Information Processing;Organismal Systems;Metabolism;MetabolismSignal transduction;Endocrine system;Global and overview maps;Lipid metabolismko04152//AMPK signaling pathway;ko03320//PPAR signaling pathway;ko01212//Fatty acid metabolism;ko01040//Biosynthesis of unsaturated fatty acidsK00507;K00507;K00507;K00507GO:0016020//membrane;GO:0016021//integral component of membraneGO:0016491//oxidoreductase activity;GO:0016717//oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of waterGO:0006629//lipid metabolic process;GO:0006633//fatty acid biosynthetic process;GO:0055114//oxidation-reduction process

  • dif
  • LN-vs-LL
  • TN-vs-TL
  • LL-vs-TL
  • LN-vs-TN

Fig 4-4-1 两组学关联载荷图


广州基迪奥生物科技有限公司



5 相关性系数模型

5.1 Pearson系数计算

皮尔逊相关系数（Pearson correlation coefficient）可用来度量两个变量之间的相互关系，代表了两个变量共变性的强弱，取值范围为[-1,+1]。计算基因表达量与代谢物丰度的pearson系数，以评估基因与代谢物的相关性[6][7][8]。

包含两种类型：

具体分析结果如下：

Tab 5-1-1 Pearson系数计算结果
关联类型 基因数据来源 代谢物数据来源 系数列表 热图
差异基因与
差异代谢物		 转录组差异集合 代谢组差异集合 dif.pearson.xls dif.heatmap.corMatrix.png
差异基因与
所有代谢物		 转录组差异集合 所有代谢物 dif_all.pearson.xls dif_all.top250.heatmap.png


差异基因并集与差异代谢物peason相关性结果如下：

Tab 5-1-2 差异基因与差异代谢物pearson系数列表
Metabolite,TranscriptGene_pathwayIDMetaboliteMetabolite_pathwayIDcorp_value
ncbi_397323K19719;04151,04510,04512,04974,05165Com_99_posC00954;00380,011000.995737907977491.0997074369041e-11
ncbi_397323K19719;04151,04510,04512,04974,05165Com_100_pos--0.9951222434316392.15683664052079e-11
ncbi_397323K19719;04151,04510,04512,04974,05165Com_871_neg--0.9940159349977185.98267926095194e-11
ncbi_100623369K06529;04360Com_938_pos--0.9934407686677559.4571794963713e-11
ncbi_110256379-Com_3450_pos--0.9925777913276351.75200919851018e-10
ncbi_100286873K00355;00130,05200,05225,05418Com_3450_pos--0.9919602493270332.60996794177091e-10
ncbi_396769K01394;04657,04668,05202,05215,05323Com_62_negC00252;005000.9918740599075962.75250281539745e-10
ncbi_100523665-Com_43_negC05598;003600.9918280500921552.83109708976583e-10
ncbi_110256379-Com_254_pos--0.991717321600513.02760963458087e-10
ncbi_100739325K07360;04014,04064,04650,04658,04659,04660,05340Com_5636_pos--0.9916996616469023.05993387972836e-10
ncbi_100515363K12326;04010,04014Com_2935_pos--0.9916593099785243.13482763249513e-10
ncbi_396769K01394;04657,04668,05202,05215,05323Com_617_posC00492;00052,020100.991646157032453.15955373922498e-10
ncbi_110261555K06521;04360Com_6471_pos--0.9914968855173433.45124624550085e-10
ncbi_100286873K00355;00130,05200,05225,05418Com_2189_pos--0.9914498050808973.54757596706865e-10
ncbi_110256218-Com_2935_pos--0.9914373479367593.57342002099186e-10
ncbi_100625219K05901;00740,00860,01100Com_2189_pos--0.9910794525413014.38268444488785e-10
ncbi_100623369K06529;04360Com_4321_posC02470;003800.990888757041564.87003737814589e-10
ncbi_100621901K16904;00240,01100Com_43_negC05598;003600.9904980386721616.00380574537078e-10
ncbi_100737690-Com_99_posC00954;00380,011000.990483559571126.04954188077389e-10
ncbi_100155948-Com_1036_negC02305;00330,011000.9904503658253176.15544396594495e-10
ncbi_100739325K07360;04014,04064,04650,04658,04659,04660,05340Com_6471_pos--0.9900914162250147.39814523013613e-10
ncbi_100626904K04386;04010,04060,04064,04380,04640,04659,04750,05146,05163,05166,05418Com_511_pos--0.9898818359336558.21147605510647e-10
ncbi_100286873K00355;00130,05200,05225,05418Com_1241_pos--0.9892264522330441.12261302184965e-09
ncbi_397323K19719;04151,04510,04512,04974,05165Com_2189_pos--0.9892165897692611.12774221083208e-09
ncbi_100737690-Com_100_pos--0.9890431394279711.22105100799898e-09
ncbi_110261555K06521;04360Com_986_neg--0.9889658158011271.26458514025912e-09
ncbi_692156K01689;00010,01100,01200,01230,03018,04066Com_99_posC00954;00380,011000.988822041443041.34882278194787e-09
ncbi_100511282K14958;04014,04625,05152Com_43_negC05598;003600.9887397569242141.39901197198018e-09
ncbi_100511285-Com_3450_pos--0.9884621640129951.57943807500204e-09
ncbi_100625457-Com_43_negC05598;003600.9882770188758441.70976537500809e-09
ncbi_396769K01394;04657,04668,05202,05215,05323Com_140_posC00208;00500,01100,02010,04742,049730.9880262094342291.89986224688306e-09
ncbi_396769K01394;04657,04668,05202,05215,05323Com_2085_posC00931;00860,01100,01110,011200.9878969454356622.0042172034861e-09
ncbi_100625219K05901;00740,00860,01100Com_1241_pos--0.9877003291680242.1716723105646e-09
ncbi_100154230K07997;04928Com_201_pos--0.9872428857866972.60469198123594e-09
ncbi_100152603K00699;00040,00053,00140,00830,00860,00980,00982,00983,01100,05204Com_43_negC05598;003600.9871269212140982.72472038535937e-09
ncbi_397614K05071;04060,04151,04630,04640,04658,04659,05200,05321Com_43_negC05598;003600.987095565117922.75792180685396e-09
ncbi_692156K01689;00010,01100,01200,01230,03018,04066Com_100_pos--0.9869411873396272.92612690427839e-09
ncbi_110261555K06521;04360Com_5636_pos--0.9868309242235383.05120207458661e-09
ncbi_110256870-Com_1603_neg---0.9865558089970983.38195409399734e-09
ncbi_100156071-Com_1603_neg---0.9865385646804283.40360095397079e-09
ncbi_106510480K04746;00533Com_99_posC00954;00380,011000.9864876494249293.46816116349112e-09
ncbi_396769K01394;04657,04668,05202,05215,05323Com_98_negC01835;02010,049730.9863028226853783.71078386574945e-09
ncbi_396769K01394;04657,04668,05202,05215,05323Com_2662_pos--0.9862888116241733.72971428041864e-09
ncbi_396769K01394;04657,04668,05202,05215,05323Com_1105_posC00762;00140,01100,04960,05200,052150.9862552808593663.77533093879632e-09
ncbi_100155736K22284;00561,01100,04979Com_1603_neg--0.9860434699480974.07388557282788e-09
ncbi_106510480K04746;00533Com_100_pos--0.9859195781822474.25705951245116e-09
ncbi_654406-Com_99_posC00954;00380,011000.9858910290913574.30018666469728e-09
ncbi_100037293K06751;04144,04145,04218,04514,04612,04650,04940,05163,05165,05166,05167,05168,05169,05203,05320,05330,05332,05416Com_6471_pos--0.9857244412799424.55884636618179e-09
ncbi_100037293K06751;04144,04145,04218,04514,04612,04650,04940,05163,05165,05166,05167,05168,05169,05203,05320,05330,05332,05416Com_986_neg--0.9855628663199634.82143901010568e-09
ncbi_100514576-Com_1603_neg---0.9855612521461594.82412191802372e-09

5.2 相关性热图

由于差异基因的数目普遍较多，不利于可视化展示关联特征，故先对所有差异基因进行筛选。取相关系数排名前50的差异基因与差异代谢物的相关性以热图展示：

Fig 5-2-1 基因表达量与代谢物丰度相关性热图图

5.3 相关性网络图

网络图可以展现处于重要关联位置的基因或代谢物，筛选出相关系数绝对值大于0.5且排名前250的差异基因与差异代谢物数据绘制网络图结果： pearson.sigma_net.html

Fig 5-3-1 基因表达量与代谢物丰度相关性网络图

广州基迪奥生物科技有限公司



6 目录结构

├── 01.expression_data                                             [组学丰度数据]
│   ├── groups.txt                                                     [分组文件]
│   ├── met.diff.xls                                                   [代谢组差异并集丰度]
│   └── rna.diff.xls                                                   [转录组差异并集丰度]
├── 02.pathway                                                     [pathway模型结果目录]
│   ├── 1.dif_pathway                                                  [差异基因与差异代谢物的分析]
│   │   └── Z-vs-ZJ                                                        [比较组Z与ZJ的分析]
│   │       ├── Z-vs-ZJ.htm                                                    [pathway富集分析]
│   │       ├── Z-vs-ZJ_map                                                    [pathway图文件]
│   │       └── Z-vs-ZJ.path.xls                                               [pathway注释]
│   ├── 2.dif_all_pathway                                              [差异基因与所有代谢物的分析]
│   │   └── ZR-vs-ZJR_all                                                  [ZR与ZJR差异基因并集与所有代谢物分析]
│   │       ├── ZR-vs-ZJR_all.htm                                              [pathway富集分析]
│   │       ├── ZR-vs-ZJR_all_map                                              [pathway图文件]
│   │       └── ZR-vs-ZJR_all.path.xls                                         [pathway注释]
│   └── 3.all_pathway                                                  [所有基因与所有代谢物的分析]
│       ├── all.htm                                                        [pathway富集分析]
│       ├── all_map                                                        [pathway图文件]
│       └── all.path.xls                                                   [pathway注释]
├── 03.o2pls                                                       [O2PLS模型结果目录]
│   ├── all.cv.stat.xls                                                [cv分析统计结果]
│   ├── component_proportions.xls                                      [模型组分统计结果]
│   ├── dif                                                            [差异基因与差异代谢物o2pls模型]
│   │   ├── dif.component_proportions.xls                                  [模型组分统计]
│   │   ├── dif.cv.stat.xls                                                [cv分析统计]
│   │   ├── o2m_loading.{pdf,png}                                          [模型loading图]
│   │   ├── top25_loading_element.{pdf,png}                                [loading值前25的关联图]
│   │   ├── dif.Metabiolite_loading.xls                                    [代谢组 loading值表]
│   │   └── dif.Transcript_loading.xls                                     [转录组 loading值表]
│   └── Z-vs-ZJ                                                        [Z与ZJ差异基因与差异代谢物o2pls模型]
│       ├── Z-vs-ZJ.component_proportions.xls                              [cv分析统计]
│       ├── Z-vs-ZJ.cv.stat.xls                                            [模型组分统计]
│       ├── o2m_loading.{pdf,png}                                          [模型loading图]
│       ├── top25_loading_element.{pdf,png}                                [loading值前25的关联图]
│       ├── Z-vs-ZJ.Metabiolite_loading.xls                                [代谢组 loading值表]
│       └── Z-vs-ZJ.Transcript_loading.xls                                 [转录组 loading值表]
├── 04.correlation                                                 [peason相关系数模型]
│   ├── 1.dif_pearson                                                  [差异基因与差异代谢物相关性结果]
│   │   ├── dif.pearson.xls                                                [peason相关性结果]
│   │   ├── dif.top250.heatmap.{pdf,png}                                    [相关性前250基因与代谢物热图]
│   │   ├── dif.top250.corMatrix.xls                                        [相关性前250基因与代谢物矩阵]
│   │   ├── top250.{Node,Edge}4cytoscape.tsv                               [相关性前250网络图绘图数据]
│   │   ├── pearson.sigma_net.html                                         [相关系数网路图]
│   │   └── pearson.sigma_net.png                                          [相关系数网路图]
│   └── 2.dif_all_pearson                                              [差异基因与所有代谢物相关性结果]
│       ├── dif_all.pearson.xls                                            [peason相关性结果]
│       ├── dif_all.top250.heatmap.{pdf,png}                              [相关性前250基因与代谢物热图]
│       ├── dif_all.top250.corMatrix.xls                                    [相关性前250基因与代谢物矩阵]
│       ├── top250.{Node,Edge}4cytoscape.tsv                               [相关性前250网络图绘图数据]
│       ├── pearson.sigma_net.html                                         [相关系数网路图]
│       └── pearson.sigma_net.png                                          [相关系数网路图]
├── index.html                                                     [html版结题报告索引]
└── src                                                                [结题报告配置文件夹]
    ├── content.html                                                       [结题报告主体html文件]
    ├── css                                                                [css配置文件夹]
    ├── doc                                                                [说明文档配置文件夹]
    ├── image                                                              [图片配置文件夹]
    └── js                                                                 [js配置文件夹]

广州基迪奥生物科技有限公司



7 附录

7.1 参考文献
7.2 帮助文档

代谢组与转录组关联分析帮助文档：help.html

代谢组与转录组关联分析英文方法：method.pdf

7.3 引用与致谢

如果您的研究课题使用了基迪奥的测序和分析服务，我们期望您在论文发表时，在Method部分或Acknowledgements部分引用或提及基迪奥公司。

以下语句可供参考:

We are grateful to/thank Guangzhou Genedenovo Biotechnology Co., Ltd for assisting in sequencing and/or bioinformatics analysis.

广州基迪奥生物科技有限公司



帮助文档