Overview

Best experienced using the browsers Chrome Firefox Safari or IE version (9,10,11)

Get an overview of Lnc2Cancer 2.0 from the Home page . The Home page is displayed in Figure 1-1 and Figure 1-2:

Figure 1-1:

1. Main functions of the database are provided in menu bar form (boxed in red).

2. Click these circles to pages including lncRNA-centric, cancer-centric, advance search, drug-resistant related results, circulating related results and prognostic related results in turn.

3. The brief introduction of Lnc2cancer 2.0.

4. A link to old version Lnc2Cancer 1.0.

5. A quick search for lncRNAs and cancers linked to Curation.

6. Quick browse and search follow different kinds of lncRNAs related with circulating, drug-resistance and prognosis.

7. Quick browse and search follow lncRNAs regulated by diverse mechanisms including miRNA, variant, TF and methylation.

8. New features of Lnc2Cancer 2.0 compared to Lnc2Cancer 1.0.

Figure 1-1

Figure 1-2:

1. Click body parts to browse major cancer types.

2. Click cancer types to browse major cancer subtypes.

3. Click middle circle to return to last level.

Figure 1-2

Search

Use the Search page to enter a keyword and filter results. Lnc2Cancer 2.0 provides general search and advanced search.

The general search page is displayed in Figure 2-1:

1. Users can input an lncRNA or cancer name to query related associations in Lnc2Cancer 2.0. Users can also input both an lncRNA and cancer name to search for associations.

2. Lnc2Cancer 2.0 also offers fuzzy keyword searching capabilities, which enables easy searching by returning the closest possible matching records.

3. The link to advanced search and help page.

Figure 2-1

The advanced search page is displayed in Figure 2-2:

1. Input your interested lncRNA.

2. Input your interested cancer.

3. Dysregulation pattern including up-regulated, down-regulated and differential expression could filter the results.

4. Diverse biomarker types of lncRNAs related with circulating, drug-resistance and prognosis could filter the results.

5. Different types of regulatory mechanisms including miRNA, TF, methylation, variant could filter the results.

6. Experimental method including RNA-seq, microarray, qPCR, RNAi and so on could filter the results.

7. Sample types including tissues, cell lines and blood could filter the results.

Figure 2-2

Results

How to read Results ?

Lnc2Cancer 2.0 results are organized in a data table, with a single association record on each line that contains lncRNA name, cancer name, methods, expression pattern, biomarker types and PubMed ID.

The result page is displayed in Figure 3-1:

1. Result for your search.

2. Click to download data.

3. Click to check the detail information of the entry.

4. Users can input keywords from any column to filter the results.

Figure 3-1

Details

How to read detail information of the entry?

Detailed information of a specific lncRNA-cancer association is displayed in Figure 4-1:

1. Users can get the basic information for the hit lncRNA.

2. Users can get the biomarker type and regulatory mechanism for the hit lncRNA.

3. Users can get the basic information for cancer.

4. Users can get detailed information for the hit lncRNA and cancer.

5. Click to check the sequence for the hit lncRNA.

6. Users can search the external annotation information for the lncRNA by clicking on the corresponding hyperlink.

Figure 4-1

Browse

How to use Browse page ?

In the LncRNA-Centric page from the drop-down menu of Browse, there are three ways to search by lncRNA name

Figure 5-1:

1. Input lncRNA name to search.

2. Browse and click to select the interested lncRNA from the drop-down 'LncRNA' list on the left-hand side of the page.

3. Browse and click to select the interested lncRNA according to its type and mechanism.

4. After step 1, 2 or 3, you will get the result page with the target lncRNA.

Figure 5-1

In the Cancer-Centric page from the drop-down menu of Browse, there are two ways to search by cancer name

Figure 5-2:

1. Input cancer name to search.

2. Browse and click to select the interested cancers from the drop-down 'cancer' list on the left-hand side of the page.

3. Browse and click to select the interested cancer according to its primary organ.

4. After step 1, 2 or 3, you will get the result page with the target cancers.

Figure 5-2

High-throughput

How to use High-throughput experiment page ?

Lists of all lncRNA expression profiles by high-throughput experiments for all cancers

Figure 6-1:

1. Click to download association data.

2. High-throughput experiment page results are organized in a data table, with a single association record on each line that contains PubMed ID, Cancer type, Sample, Experiment design, Sample case, Sample control, Sample size, Number of up-regulated lncRNAs, Number of down-regulated lncRNAs and Data availability.

3. Click to download the original lncRNA profiles from GEO.

4. Users can input keywords from any column to filter the results.

Figure 6-1

Lnc-Cancer Score

Get an overview of Lnc-Cancer_Score.

Score= N*(C+B+T)

N:the number of lncRNA-cancer association for your search

C:0 or 1; if the lncRNA-cancer association had been verified in cancer cell lines.

B:0 or 1; if the lncRNA-cancer association had been verified in cancer blood.

T:0 or 1; if the lncRNA-cancer association had been verified in cancer tissues.

e.g. The association between MALAT1 and multiple myeloma are verified in 7 publications. For the publication numbered 25369863, MALAT1 is associated with multiple myeloma verified in tissue. Thus we calculate the score as follow:

Score=7*(0+0+1)=7

Figure 7-1:

1. Users can input an interested lncRNA or/and cancer name.

2. The number of lncRNA-cancer verified entries in Lnc2Cancer 2.0 for your search.

3. If the lncRNA-cancer association had been verified in cancer cell lines, tissues and blood.

4. The scores for the lncRNA-cancer associations. Users could rank the lncRNA-cancer association by scores.

Figure 7-1