ATC-Specific TP53 Profiling: microRNA Interactions & Mutations 

Aim of the Tool:

This web‑based tool is designed to examine—at high resolution—the 3′‑UTR region of the TP53 gene, which plays a critical role in aggressive tumors such as anaplastic thyroid cancer (ATC). TP53 serves as the “central command” for cellular stress responses and tumor‑suppression mechanisms; therefore, even small alterations within its 3′‑UTR can dramatically affect TP53 protein levels.

Why the 3′‑UTR?

• Post‑transcriptional control hub: miRNAs bind to the 3′‑UTR to regulate TP53 mRNA stability and translational efficiency.

• The “hidden” impact of somatic mutations: Single‑nucleotide changes that disrupt miRNA binding—without touching the coding region—can disable the gene’s tumor‑suppressor function.

Value Added by the Tool

1. Full‑length alignment: The patient‑specific 3′‑UTR sequence supplied by the user is aligned nucleotide‑by‑nucleotide to the reference TP53 sequence, capturing single‑nucleotide variants (SNVs) and small indels comprehensively.

2. miRNA seed overlap detection: The embedded MIRNA_CSV list contains the seed positions of ~100 miRNAs that are experimentally validated or predicted to bind TP53. The tool detects in real time whether any mutation intersects these seed windows.

3. Pre‑computed miRES score: Calculated as the product of binding strength (B), functional impact (F), pathogenicity linkage (P) and conservation (C). Thus, even before a mutation‑specific recalculation, interactions are already ranked by their clinical relevance.

4. Fast and platform‑agnostic: All computations run client‑side in JavaScript—no server load, high privacy.

5. Research‑to‑clinic bridge:

   • Scientist: Instantly receives a summary table to hypothesize mutation‑miRNA relationships.

   • Molecular pathology lab: Rapidly selects which miRNAs will proceed to functional testing.

   • Clinician: Can incorporate potential prognostic/predictive biomarkers into the report.

Mandatory Criteria for the Patient TP53 3′‑UTR Sequence You Paste into the Tool

1. Full‑length match
   • Reference sequence (REF_SEQ) length = 1188 nucleotides.
   • The patient sequence must also be exactly 1188 nt; even a single extra or missing base will trigger a “Length mismatch!” error.

2. DNA letters only (A T G C)
   • The RNA symbol U and the ambiguous base N are not accepted.
   • Case‑insensitive—the tool converts everything to uppercase.

3. Spaces and line breaks allowed; numbers & symbols forbidden
   • Multi‑line FASTA blocks, tabs, and other whitespace are automatically stripped.
   • Digits (1, 2, 3 …), punctuation (., ;), emojis, etc. are removed; otherwise they can cause a length error.

4. Optional FASTA header
   • You may add a header such as “>Sample_007” on the first line; the code ignores it.
   • Whether or not you include a header, you must paste only one sequence.

5. One sequence, one patient
   • Do not paste multiple sequences in the same box—the analysis will consider only the first 1188 nt.

6. DNA format ≠ cDNA
   • Provide the genomic TP53 3′‑UTR; do not include introns, promoter, coding region, or a poly‑A tail.

7. Pre‑check recommendation
   • Before pasting, count the sequence length in a text editor (Notepad++ → “Length” indicator).
   • If the GC‑content is not ~50 %, you may have copied the reference from the wrong location.

miRES Score:

Binding Strength ( B ) : Indicates how strongly a miRNA binds to its target site in the TP53 3′-UTR. 

• The binding energy (ΔG) or binding score produced by algorithms such as RNAhybrid, TargetScan, and similar tools is used.

• The ΔG value is normalized on a relative scale

Functional Impact ( F ) : The miRNA’s direct or indirect ability to repress or support TP53. 

• A five-level categorical system is used, based on literature and experimental data: 

  • 1. Direct OG - miRNA has been shown to directly repress TP53 expression - 1.0

  • 2. Indirect OG - miRNA has been shown to suppress TP53 pathways indirectly (e.g., by activating MDM2) - 0.85 

  • 3. Unclear / Predicted - Functional effect unknown; only in silico evidence available - 0.70 

  • 4. Indirect TS - miRNA has been shown to support TP53 pathways indirectly (e.g., via PTEN, ATM) - 0.60 

  • 5. Direct TS - miRNA has been shown to directly increase TP53 expression - 0.50 

Pathogenicity Link ( P ) : The strength of the miRNA’s association with ATC, thyroid cancers, or cancer in general. 

• 1. ATC (Anaplastic Thyroid Cancer) + OG - 2.0 

• 2. ATC + TS - 0.001 

• 3. Thyroid cancer + OG - 1.5 

• 4. Thyroid cancer + TS - 0.01 

• 5. INSUFFICIENT EXPERIMENTAL EVIDENCE - 0.5

  • For this type of miRNA, the following experimental evidence is not available in the current literature: 

    • qRT-PCR / Northern blot (expression level analysis) 

    • Functional cell culture assays (proliferation, apoptosis, migration/invasion, colony formation) 

    • Luciferase reporter assay (target gene validation) 

    • Western blot / qRT-PCR (target gene/protein expression analysis) 

    • Rescue experiments (reversal of effect via target gene manipulation) 

    • Animal models (in vivo) (tumor growth/metastasis function) 

    • Immunohistochemistry (IHC) (tissue-level protein validation) 

    • Therefore, there is no functional or clinical role experimentally demonstrated for this miRNA. Only sequence/database registration or in silico predictions are available. 

• 6. General cancer + OG - 1.0 

• 7. General cancer + TS  -  0.1

Conservation Score ( C ) : Indicates how conserved the miRNA target region is across different species. 

• The PhyloP genomic conservation score is used.

• C is the normalized (0.1 - 0.6) mean PhyloP value of all bases within the target region.