Browse Page

  • (A) The interface of browse page.
    • (Ⅰ) Select species, type of tissue/cell lines and tissue/cell lines by drop-down menus.
    • (Ⅱ) Choose the type of loops by drop-down menu.
    • (Ⅲ) Set q value by slider to filter the different levels of statistically significant FFLs.
    • (Ⅳ) Users are able to select the all, conserved or poorly conserved miRNA target genes to filter the results.
    • (Ⅴ) Confidence score of microRNA target genes can be decided by adjusting the threshold of target score in range from 1.0 to 3.0, the higher the value of score, the higher confidence of miRNA target genes.
  • (B) An example of TF-enhancer-miRNA FFL (FOXA1-enH1004940-miR-26a-2-3p)
    • Clicking on the drop-down list of FOXA1, enH1004940 and miR-26a-2-3p, users are accessible to more detailed information and external links of each element as shown in (Ⅰ-Ⅲ).
    • (Ⅳ) The page will redirect to the detailed page for showing all loops an element involved in. Taking FOXA1 as example, clicking link of ‘All loops involving FOXA1’, the page will turn to the new page which includes all types of loops which FOXA1 involved in.

Search Page

  • (A) Usage example for search page.
    • (Ⅰ) Select the species by drop-down menu.
    • (Ⅱ) Select the type of elements users want to search and input Name/ID to search.
    • (Ⅲ) Users can customize results for conserved miRNA targets only, poorly conserved only or all miRNA target genes. After clicking on the 'Search' button, it will be redirected to detailed page shown as top right corner.
  • (B) If location information is inputted, it will present the page of the same type of element that overlap with the input one. And there is a link to the detailed page of the element in the drop-down list.

API usage

We provide two api endpoints for users.

(1) /EnhFFL/api/browse/

API usage

Retrive data by specific relationship

Parameters are listed:

  • relation: for looping relationship types, inluding 4 types

    • emg: Enhancer-miRNA-Gene
    • tem: TF-Enhancer-miRNA
    • teg: TF-Enhancer-Gene
    • te: TF-Enhancer
  • species: human or mouse

  • conserve: different meaning for emg and other three

    • For emg:

      • all: use all the target genes of miRNA
      • Conserved: conserved target genes of miRNA
      • Non Conserved:
    • For tem, teg, te: this parameter represents the sources of TFs

      • all
      • experiment
      • predicted
  • score: select the Enhancer-miRNA target score 1.0~3.0 step by 0.5

  • qvalue: select the relationships with qValue lower than thredhold

  • tissue: for different tissues, please use the full cell line name

    • eg: BI_Adipose_Nuclei - Adipose, please use BI_Adipose_Nuclei as condition

(2) /EnhFFL/api/details/

Retrive all the relationships that specific element involved

Parameters are listed:

  • subtype: for which kind of element that you want to search

    • enhancer
    • tf
    • mirna
    • gene
  • term: searching term

    • enhancer ID for enhancers
    • TF name for TFs
    • miRRase ID or miRNA name for miRNAs
    • Ensembl ID or Gene name for genes
  • species: human or mouse

  • conserve: For tem, teg, te, this parameter represents the sources of TFs

    • all
    • experiment
    • predicted
  • enhCon:

    • all: use all the target genes of miRNA
    • Conserved: conserved target genes of miRNA
    • Non Conserved
  • tissue: see before

  • relation: additional, if used, return specific kind of loops that element involved



Southwest Jiaotong University
School of Life Sciences and Bioengineering
Chengdu, Sichuan, China