国家自然科学基金(61532014,61571163,61402132,61671189)
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Figure 1
(Color online) Progress of core module mining method
Figure 2
(Color online) lncRNA experimental result. (a) Results while including lncRNA and random data; protectłinebreak (b) results while excluding lncRNA data
Figure 3
Core gene module with regulating factors
Figure 4
Core gene module
Figure 5
Result of distinguish normal and tumor samples according to core genes
Figure 6
Result of function and pathway analysis
Figure 7
(Color online) TCGA survival analysis result. (a) 15-genes; (b) 12-genes
Figure 8
(Color online) GEO survival analysis result. (a) 15-genes GSE8894; (b) 15-genes GSE17710; (c) 12-genes GSE8894; (d) 12-genes GSE17710
| Gene | Chromosome | Start point | End point |
| TP53 | hs17 | 7668402 | 7687550 |
| CDKN2A | hs9 | 21967752 | 21995043 |
| DROSHA | hs5 | 31400494 | 31532175 |
| DAB2 | hs5 | 39371674 | 39425233 |
| SMC4 | hs3 | 160399304 | 160434962 |
| PRKCI | hs3 | 170222432 | 170305982 |
| SKIL | hs3 | 170357678 | 170396849 |
| ECT2 | hs3 | 172750682 | 172829273 |
| DVL3 | hs3 | 184155311 | 184173614 |
| AP2M1 | hs3 | 184174846 | 184184091 |
| DNAJB11 | hs3 | 186570676 | 186585800 |
| AHSG | hs3 | 186612928 | 186621318 |
| CCDC50 | hs3 | 191329082 | 191398670 |
| TNK2 | hs3 | 195863364 | 195909009 |
| DLG1 | hs3 | 197042560 | 197299272 |
| $\varepsilon$: 扫描半径参数 |
| MinPts: 邻域密度阀值 |
| $1$. 创建空间为$n\times~n$的二维矩阵dis用于存储关键基因间距离; |
| $2$. 计算dataset中关键基因间距离并保存到dis 矩阵; |
| $3$. 对于dataset中的对象,根据dis标记满足$\varepsilon$范围内密度大于Minpts 的对象为core point; |
| $4$. 标记core point在$\varepsilon$范围内的非core point对象为border point; |
| $5$. 标记dataset中既不是core point也不是border point的对象为noise point; |
| $6$. 标记dataset中所有对象为unvisited; |
| $7$. for core point中的每个对象$p~$ //深度优先连接所有core point |
| $8$. 创建栈Stack; |
| $9$. if $p$是visited |
| $10$. Continue; |
| $11$. 将$p$标记为visited压入Stack |
| $12$. while(Stack不为空) |
| $13$. $v$ $\leftarrow$ Stack弹出栈顶; |
| $14$. for $v$邻域内的每个对象$q$ |
| $15$. if $q$是visited |
| $16$. Continue; |
| $17$. 将$q$纳入$p$所在cluster; |
| $18$. 将$q$标记为visited; |
| $19$. 将$q$压入Stack; |
| $20$. end for |
| $21$. end while |
| $22$. end for |
| $23$. for border point中的每个对象$b$ |
| $24$. 将$b$纳入$\varepsilon$范围内任意core point所属cluster; |
| $25$. end for |
| $26$. 输出dataset中core point 与border point 对象以及其对应的cluster. |
| ID | Term |
| GO:0035556 | Intracellular signal transduction |
| hsa04144 | Endocytosis |
| GO:0032147 | Activation of protein kinase activity |
| hsa05203 | Viral carcinogenesis |
| GO:0043065 | Positive regulation of apoptotic process |
| GO:0046677 | Response to antibiotic |
| GO:0071479 | Cellular response to ionizing radiation |
| GO:0090004 | Positive regulation of establishment of protein localization to plasma membrane |
| GO:0071158 | Positive regulation of cell cycle arrest |
| GO:0042326 | Negative regulation of phosphorylation |
| hsa04390 | Hippo signaling pathway |
| GO:0045197 | Establishment or maintenance of epithelial cell apical/basal polarity |
| GO:0090399 | Replicative senescence |
| GO:0045893 | Positive regulation of transcription, DNA-templated |
| GO:0007050 | Cell cycle arrest |
| GO:1903077 | Negative regulation of protein localization to plasma membrane |
| hsa05166 | HTLV-I infection |
| GO:0070830 | Bicellular tight junction assembly |
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