Document


1. Overview

Welcome to LncMAP! Here is a step to step introduction about how to use the web to search the transcription factors(TF) and gene regulations that are mediated by lncRNAs in cancer. The users can search the lncRNA-TF-gene triplets identified in 20 cancers in this web. At the same time, the users can obtain the information between drugs and lncRNAs, survival analysis and tf-gene regulation of pan-cancer.

2. LncRNA-TF-Gene Triplet

The LncMAP provides an interface to retrieve the information about the lncRNA-TF-gene triplets in cancer. The current release of LncMAP mainly contains the results in 20 kinds of cancer. Users can search by individual lncRNA or by individual TF or by individual gene to view the lncRNA-TF-gene association in a certain cancer. Here, we provide an example where users can click on "examples" and "submit", to check out the information about triplets.

2.1 The Results of LncRNA-TF-Gene Triplet

The query results are as follows: including cancer type, the information of lncRNA , the information of TF, the information of Gene, the action modulator of lncRNA. When the users click on "more...", detailed information will be obtained. At the same time, we rank the FDR, and take the top 30 lncRNA-TF-gene triplets to build the network. Clicking 'LncRNA-TF-Gene Network' will show the network,where the square represents lncRNA, the triangle represents TF, and the circle represents the gene.

Note: '-' and '+' represent the sign of the correlation coefficient; and the '--' and '++' represent the increased correlation.

2.2 The LncRNA-TF-Gene Network

At the same time, we rank the FDR, and take the top 30 lncRNA-TF-gene triplets to build the network. Clicking 'LncRNA-TF-Gene Network' will show the network,where the square represents lncRNA, the triangle represents TF, and the circle represents the gene.

2.3 The Detail Information of Triplet

The table of detail information shows the whole results of the lncRNA-TF-gene triplet, the first row shows the abbreviation name of the cancer type, the second row shows lncRNA ID and the next row shows lncRNA symbol. The fourth row shows TF ID and the next row shows TF symbol. The sixth and seventh rows show gene ID and gene symbol. The eighth shows lncRNA type, when the mouse on the lncRNA type, will show cancer types, which is involved in lncRNA as a triplet modulator. The ninth and tenth rows show correlation coefficient in lncRNA low and high expression group. The eleventh row shows the rewiring score that we defined and rewire(TF-gene) which ranges between 0 and 1, with larger value indicating more rewiring effect between TF and gene. The twelfth and thirteenth rows show p value and FDR. The fourteenth row shows lncRNA modulator. The fifteenth and sixteenth rows show Fisher transformation of correlation coefficient in lncRNA low and high expression group. The seventeenth and last rows show the probability in discovery and validation set. In addition, we have added three pictures, visualization of the correlation coefficient in lncRNA expression group, visualization of lncRNA expression and visualization of gene expression, respectively.

2.4 The Correlation Coefficient in LncRNA Expression Group

2.5 The Expression Pattern of LncRNA

2.6 The Expression Pattern of TF and Gene

3. Drug-LncRNA

The LncMAP also provides an interface to retrieve the results about calculating the Spearman correlation coefficient between lncRNA expression levels and the IC50 values of 24 drugs. Users can search by individual lncRNA or by individual drug to view the relationship between drug and lncRNA.

3.1 The Results of Drug-LncRNA

Here, we provide an example to check out the result, as follows, drug, the information of lncRNA, Spearman correlation coefficient, p value and FDR.

4. Survival Analysis

We integrated the clinical data to explore the prognostic associated lncRNA-TF-gene triplets. Thus, here we also exhibit the results of the survival analysis of triplets in each cancer. Users can search by individual lncRNA or by individual TF or by individual gene to view the results in a certain cancer.

4.1 The results of Survival Analysis

Equally, we also use an example to reveal the results of the survival analysis, as follows: cancer name, the information of triplets, p-value of the discovery dataset, p-value of the validation dataset.

5. TF-Gene

Users can also view TF-gene regulations in a specific cancer context. Users can search by individual TF or by individual gene to view the results in a certain cancer.

5.1 The results of TF-Gene

Similarly, results include cancer name, the information of TF and gene, the regression coefficient, p-value and FDR.

6. Cancer name abbreviations

Abbreviations Cancer
BLCA Bladder Urothelial Carcinoma
BRCA Breast invasive carcinoma
CESC Cervical squamous cell carcinoma and endocervical adenocarcinoma
COAD Colon adenocarcinoma
GBM Glioblastoma multiforme
HNSC Head and Neck squamous cell carcinoma
KICH Kidney Chromophobe
KIRC Kidney renal clear cell carcinoma
KIRP Kidney renal papillary cell carcinoma
LGG Brain Lower Grade Glioma
LIHC Liver hepatocellular carcinoma
LUAD Lung adenocarcinoma
LUSC Lung squamous cell carcinoma
OV Ovarian serous cystadenocarcinoma
PRAD Prostate adenocarcinoma
READ Rectum adenocarcinoma
SKCM Skin Cutaneous Melanoma
STAD Stomach adenocarcinoma
THCA Thyroid carcinoma
UCEC Uterine Corpus Endometrial Carcinoma

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