Background
Methods
Approach overview
Bio-ontologies underlying OmniSearch
Semantics-oriented MeSH-term filtering mechanisms
Results
Results from manual background literature search
More likely regulating miRNAs through two rounds of the MeSH-term filtering
miRNA | Number of reporting databases | Number of total targets supported by at least one publication |
---|---|---|
hsa-miR-124-3p | 3 | 15 |
hsa-miR-124-5p | 2 | 0 |
hsa-miR-128-3p | 3 | 5 |
hsa-miR-142-3p | 4 | 69 |
hsa-miR-15b-3p | 2 | 0 |
hsa-miR-17-5p | 3 | 84 |
hsa-miR-18a-3p | 3 | 4 |
hsa-miR-182-5p | 3 | 16 |
hsa-miR-193a-3p | 4 | 17 |
hsa-miR-218-5p | 3 | 2 |
hsa-miR-221-3p | 3 | 1 |
hsa-miR-335-5p | 3 | 8 |
hsa-miR-532-5p | 3 | 5 |
hsa-miR-550a-3p | 2 | 0 |
hsa-miR-625-5p | 2 | 1 |
hsa-miR-633 | 2 | 0 |
hsa-miR-638 | 2 | 3 |
hsa-miR-708-5p | 3 | 2 |
Average | 3 | 13 |
Total | – | 232 |
miRNA | Number of predicted targets | Number of validated targets |
---|---|---|
hsa-miR-142-3p | 12 | 11 |
hsa-miR-17-5p | 7 | 11 |
hsa-miR-18a-3p | 2 | 2 |
hsa-miR-128-3p | 4 | 0 |
hsa-miR-193a-3p | 4 | 1 |
hsa-miR-124-3p | 0 | 7 |
hsa-miR-182-5p | 4 | 4 |
hsa-miR-335-5p | 1 | 0 |
hsa-miR-708-5p | 0 | 1 |
hsa-miR-625-5p | 1 | 0 |
hsa-miR-218-5p | 1 | 0 |
hsa-miR-532-5p | 0 | 1 |
hsa-miR-221-3p
|
0
|
0
|
hsa-miR-633
|
0
|
0
|
hsa-miR-550a-3p
|
0
|
0
|
hsa-miR-638
|
0
|
0
|
hsa-miR-124-5p
|
0
|
0
|
hsa-miR-15b-3p
|
0
|
0
|
Total | 36 | 38 |
miRNA | Number of predicted targets | Number of validated targets |
---|---|---|
hsa-miR-142-3p | 5 | 4 |
hsa-miR-17-5p | 3 | 3 |
hsa-miR-18a-3p | 2 | 0 |
hsa-miR-128-3p | 1 | 0 |
hsa-miR-193a-3p | 0 | 1 |
hsa-miR-124-3p
|
0
|
0
|
hsa-miR-182-5p
|
0
|
0
|
hsa-miR-335-5p
|
0
|
0
|
hsa-miR-708-5p
|
0
|
0
|
hsa-miR-625-5p
|
0
|
0
|
hsa-miR-218-5p
|
0
|
0
|
hsa-miR-532-5p
|
0
|
0
|
Total | 11 | 8 |
Discussion
Analysis of miRNA: Target regulation via semantic search
More likely regulating miRNAs | Computationally predicted targets | Biologically validated targets |
---|---|---|
hsa-miR-142-3p | • ASH1L [ash1 (absent, small, or homeotic)-like (Drosophila)] • CP [ceruloplasmin (ferroxidase)] • MLLT1 [myeloid/lymphoid or mixed-lineage leukemia; translocated to, 1] • MLLT4 [myeloid/lymphoid or mixed-lineage leukemia; translocated to, 4] • SAG [S-antigen; retina and pineal gland (arrestin)] | • CCNT2 [cyclin T2] • EGR2 [early growth response 2] • HOXA10 [homeobox A10] • HOXA7 [homeobox A7] |
hsa-miR-17-5p | • AGO2 [argonaute 2, RISC catalytic component] • BCR [breakpoint cluster region] • NPM1 [nucleophosmin (nucleolar phosphoprotein B23, nunatrin)] | • E2F1 [E2F transcription factor 1] • RUNX1 [runt related transcription factor 1] • TP53 [tumor protein p53] |
hsa-miR-18a-3p | • ARHGAP26 [Rho GTPase activating protein 26] • IMPACT [impact RWD domain protein] | None |
hsa-miR-128-3p | • PHF6 [PHD finger protein 6] | None |
hsa-miR-193a-3p | None | • MCL1 [myeloid cell leukemia 1] |
Effective and efficient analysis in OmniSearch
miRNA under search | Percentage of saved time on obtaining search results | Percentage of saved time on conducting pathway analysis | Percentage of saved time on comparing results across different target databases |
---|---|---|---|
hsa-miR-142-3p | 69% | 59% | 57% |
hsa-miR-17-5p | 71% | 53% | 63% |
hsa-miR-18a-3p | 53% | 63% | 59% |
hsa-miR-128-3p | 68% | 58% | 70% |
hsa-miR-193a-3p | 73% | 51% | 64% |
Average for five miRNAs | 67% | 57% | 63% |