今天我们来介绍一个功能强大的网站Oncomir:http://www.oncomir.org/
![clip_image002.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_2_20171023095611567](https://www.jingege.wang/wp-content/uploads/2020/05/15573052385706.jpg)
这是我们Oncomir的主页,下面我们来看网站的功能。
在数据库的左侧是不同的功能选项,我们看到首先是:
![clip_image003.png http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_3_20171023095612333](https://www.jingege.wang/wp-content/uploads/2020/05/15573052613109.png)
1. Search by miRNA: 根据miRNA进行搜索;
2. Search by Cancer Type:根据肿瘤类型进行搜索;
3. Search for miRNA-targetcorrelation:搜索miRNA和靶基因的相关性;
4. Survival SignatureAnalysis:生存分析;
5. Clustering Analysis:聚类分析。
第一个:根据miRNA进行搜索,
1) TumorDevelopment:查询某条miRNA在肿瘤组和对照组是否表达异常:
![clip_image005.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_4_20171023095612583](https://www.jingege.wang/wp-content/uploads/2020/05/15573053235374.jpg)
以案例的miRNA hsa-miR-92a-3p为例,单击Retrieve cancer types:
![clip_image007.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_5_20171023095612849](https://www.jingege.wang/wp-content/uploads/2020/05/15573053385994.jpg)
结果显示hsa-miR-92a-3p在14个肿瘤里面显著表达异常。
2)TumorStage and Grade:
![clip_image009.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_6_20171023095613286](https://www.jingege.wang/wp-content/uploads/2020/05/15573053873067.jpg)
还是hsa-miR-92a-3p,所有肿瘤:
![clip_image011.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_7_20171023095613552](https://www.jingege.wang/wp-content/uploads/2020/05/15573054089143.jpg)
就可以看到miRNA在不同肿瘤里面的情况,比如与BRCA乳腺癌N、T和分级相关。
3) Survival Outcome:生存状态
![clip_image013.png http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_8_2017102309561436](https://www.jingege.wang/wp-content/uploads/2020/05/15573054173947.png)
这是结果:
![clip_image015.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_9_20171023095614302](https://www.jingege.wang/wp-content/uploads/2020/05/15573054253511.jpg)
四个肿瘤里面的数据。
4) ExpressionProfile:
![clip_image017.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_10_20171023095614724](https://www.jingege.wang/wp-content/uploads/2020/05/15573054354361.jpg)
我们选择所有肿瘤:
![clip_image019.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_11_201710230956155](https://www.jingege.wang/wp-content/uploads/2020/05/15573054548664.jpg)
miRNA在所有肿瘤里面的表达数据。
第二个:根据肿瘤类型进行搜索。
1)TumorDevelopment,选择所有肿瘤:
![clip_image021.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_12_20171023095615380](https://www.jingege.wang/wp-content/uploads/2020/05/15573054856816.jpg)
结果:
![clip_image023.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_13_20171023095615692](https://www.jingege.wang/wp-content/uploads/2020/05/15573054939225.jpg)
在各个肿瘤里面共有6182条miRNA表达差异(与正常相比),大家在做课题前就可以直接查询选miRNA了。
2)TumorStage and Grade。我们选择所有肿瘤的M分期:
![clip_image025.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_14_2017102309561636](https://www.jingege.wang/wp-content/uploads/2020/05/15573055023965.jpg)
结果:
![clip_image027.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_15_20171023095616317](https://www.jingege.wang/wp-content/uploads/2020/05/15573055114776.jpg)
这样我们是不是就可以找到与转移相关的miRNA了?
3)SurvivalOutcome:
![clip_image029.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_16_20171023095616802](https://www.jingege.wang/wp-content/uploads/2020/05/15573055243962.jpg)
结果:
3820条miRNA在各肿瘤患者不同生存状态中的显著差异。
4) ExpressionProfile:
![clip_image033.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_18_20171023095617318](https://www.jingege.wang/wp-content/uploads/2020/05/15573055566337.jpg)
所有的miRNA在所有收录的肿瘤里面表达:
![clip_image035.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_19_20171023095617536](https://www.jingege.wang/wp-content/uploads/2020/05/15573055643018.jpg)
也可以自己提交名单:
![clip_image037.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_20_20171023095617989](https://www.jingege.wang/wp-content/uploads/2020/05/15573055731708.jpg)
结果:
![clip_image039.png http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_21_20171023095618271](https://www.jingege.wang/wp-content/uploads/2020/05/15573055807506.png)
第三个:搜索miRNA和靶基因的相关性。
1) Searchby miRNA:根据miRNA搜索。
![clip_image041.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_22_20171023095618411](https://www.jingege.wang/wp-content/uploads/2020/05/15573055882748.jpg)
结果:
![clip_image043.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_23_20171023095618630](https://www.jingege.wang/wp-content/uploads/2020/05/15573055965108.jpg)
不仅有基因名字,还有靶基因表达与miRNA表达的相关性等数据。
2)Search byGene:根据基因搜索:
![clip_image045.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_24_20171023095618989](https://www.jingege.wang/wp-content/uploads/2020/05/15573056068844.jpg)
同样也可以实现:
![clip_image047.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_25_20171023095619130](https://www.jingege.wang/wp-content/uploads/2020/05/15573056169382.jpg)
第四个:生存分析。
1)Pre-calculatedsignatures:预计算的指标。
![clip_image049.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_26_20171023095619427](https://www.jingege.wang/wp-content/uploads/2020/05/15573056555896.jpg)
我们选择肺腺癌,经过计算的miRNA表达与生存之间的关系:
![clip_image051.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_27_20171023095619583](https://www.jingege.wang/wp-content/uploads/2020/05/15573056676873.jpg)
大家可以直接看到风险公式里面各miRNA前面的权重数值:
![clip_image053.png http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_28_20171023095619896](https://www.jingege.wang/wp-content/uploads/2020/05/1557305674483.png)
2)Customsignatures:自定义miRNA。
![clip_image055.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_29_2017102309562036](https://www.jingege.wang/wp-content/uploads/2020/05/15573056823846.jpg)
输入我们的miRNA和权重数值,不输入权重数值会直接默认计算好的指标:
![clip_image057.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_30_20171023095620302](https://www.jingege.wang/wp-content/uploads/2020/05/15573056903435.jpg)
这里大家可以直接通过多条miRNA的表达组合来对患者预后进行指征。
第五个功能:聚类分析。
有了miRNA在各肿瘤的表达后,我们可以对输入的miRNA进行分层聚类:
![clip_image059.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_31_20171023095620630](https://www.jingege.wang/wp-content/uploads/2020/05/1557305709434.jpg)
结果:
![clip_image061.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_32_20171023095620989](https://www.jingege.wang/wp-content/uploads/2020/05/15573057238433.jpg)
也可以对所有的miRNA进行分层聚类:
![clip_image063.jpg http://image109.360doc.com/DownloadImg/2017/10/2309/114233422_33_20171023095621318](https://www.jingege.wang/wp-content/uploads/2020/05/1557305739336.jpg)
好了,这个网站的功能就介绍到这里了,大家使用的时候推荐chrome浏览器。
另外,吃水不忘挖井人,原文:OncomiR: An onlineresource for exploring pan-cancer microRNAdysregulation.Bioinformatics. 2017 Oct 3. doi:10.1093/bioinformatics/btx627.记得引用。