micro-RNA Heart Transplantation

Data importing

✓ Configuration loaded successfully
✓ Configuration for transplantation loaded successfully

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LOADING AND PROCESSING DATA
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Loading phenotable data...
   File: /Users/dariakilina/GitHub/ncRNA_pipeline/Transplantation/data/phenotable.tsv 
   ✓ Loaded 30 samples
   ✓ Groups: ACR, AMR, CAV, NR

 Loading counts data...
   File: /Users/dariakilina/GitHub/ncRNA_pipeline/data/raw/miR.Counts.csv 
   ✓ Loaded 2731 features × 49 samples

 Cleaning sample names...
   ✓ No cleaning needed

🔗 Matching samples between counts and phenotable...
   Counts:    49 samples
   phenotable: 30 samples
   Common:    30 samples
 19 counts samples not in phenotable
   ✓ Sample order verified

 Filtering low-expressed features...
   Smallest group size: 6 samples
   Threshold: >= 10 counts in >= 6 samples
   ✓ Kept 561 / 2731 features (20.5%)
   ✓ Removed 2170 low-expressed features

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✅ DATA PROCESSING COMPLETE
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Final dataset: 561 features × 30 samples
Groups: ACR, AMR, CAV, NR
Samples per group:

ACR AMR CAV  NR 
  8   6   7   9 

📋 Loading sample annotation...
   File: /Users/dariakilina/GitHub/ncRNA_pipeline/data/raw/annotation.report.csv 
   ✓ Loaded 49 samples × 15 columns
   ✓ Retained 9 columns after filtering

🔗 Matching annotation with phenotype...
   Annotation samples: 49
   Phenotype samples:  30
   Common samples:     30
   ✓ Annotation successfully aligned

Venn plot (>150 counts)

Unique miRs

$ACR
 [1] "hsa-miR-1255a"    "hsa-miR-330-5p"   "hsa-miR-331-3p"   "hsa-miR-4433b-3p" "hsa-miR-487b-3p"  "hsa-miR-493-3p"  
 [7] "hsa-miR-493-5p"   "hsa-miR-610"      "hsa-miR-6513-3p"  "hsa-miR-708-3p"  

$AMR
 [1] "hsa-miR-194-3p"                             "hsa-miR-3065-5p"                           
 [3] "hsa-miR-3128"                               "hsa-miR-326-3p"                            
 [5] "hsa-miR-365a-3p/365b-3p"                    "hsa-miR-370-3p"                            
 [7] "hsa-miR-378a-5p"                            "hsa-miR-378i"                              
 [9] "hsa-miR-455-5p"                             "hsa-miR-485-5p"                            
[11] "hsa-miR-499a-5p"                            "hsa-miR-548ae-3p/548aj-3p/548aq-3p/548x-3p"
[13] "hsa-miR-548ah-3p/548am-3p"                  "hsa-miR-618-5p"                            

$CAV
 [1] "hsa-miR-10a-3p"  "hsa-miR-1303-3p" "hsa-miR-218-5p"  "hsa-miR-29c-5p"  "hsa-miR-3135a"   "hsa-miR-362-5p"  "hsa-miR-4638-3p"
 [8] "hsa-miR-4755-3p" "hsa-miR-539-3p"  "hsa-miR-570-3p"  "hsa-miR-641"    

$NR
 [1] "hsa-miR-190b-5p"           "hsa-miR-193a-3p"           "hsa-miR-219a-1-3p"         "hsa-miR-3163"             
 [5] "hsa-miR-3691-5p"           "hsa-miR-4659a-3p/4659b-3p" "hsa-miR-4772-5p"           "hsa-miR-4999-5p"          
 [9] "hsa-miR-6511b-5p"          "hsa-miR-652-5p"            "hsa-miR-660-3p"            "hsa-miR-6741-3p"          
[13] "hsa-miR-6780a-5p"          "hsa-miR-6884-5p"           "hsa-miR-7705"             

Barplots

Run Differential Expression Analysis

Rank of model matrix: 4 
Number of columns: 4 
class: DESeqDataSet 
dim: 561 30 
metadata(1): version
assays(6): counts mu ... replaceCounts replaceCooks
rownames(561): hsa-let-7a-3p hsa-let-7a-5p/7c-5p ... hsa-miR-99b-3p hsa-miR-99b-5p
rowData names(31): baseMean baseVar ... maxCooks replace
colnames(30): 182_S25_R1_001 112_S27_R1_001 ... 103_S17_R1_001 128_S8_R1_001
colData names(4): sample condition sizeFactor replaceable

transformation

• The plot should show a nearly horizontal line, meaning the SD is independent of the mean expression. • This means the transformation has successfully stabilized the variance, making the data more suitable for further analysis.

Samples: 30 
Genes: 561 
Using rlog transformation

$transformed
class: DESeqTransform 
dim: 561 30 
metadata(1): version
assays(1): ''
rownames(561): hsa-let-7a-3p hsa-let-7a-5p/7c-5p ... hsa-miR-99b-3p hsa-miR-99b-5p
rowData names(32): baseMean baseVar ... replace rlogIntercept
colnames(30): 182_S25_R1_001 112_S27_R1_001 ... 103_S17_R1_001 128_S8_R1_001
colData names(4): sample condition sizeFactor replaceable

$method
[1] "rlog"

PCA plot

Plot a heatmap of most variable genes

Plot of the distance between samples heatmap

Results

Significant results saved to: results/results_humoral.csv 
Significant results saved to: results/sign_results_humoral.csv 
Significant results saved to: results/results_cellular.csv 
Significant results saved to: results/sign_results_cellular.csv 
Significant results saved to: results/results_CAV.csv 
Significant results saved to: results/sign_results_CAV.csv 

MA plot

Volcano plot

Create boxplot for specific gene

Plot a heatmap of diff expressed genes

NULL
NULL

Enrichment analysis

Searching for targets

Searching mirecords ...
Searching mirtarbase ...
Searching tarbase ...
Searching mirecords ...
Searching mirtarbase ...
Searching tarbase ...

No significant miRNAs found in cellular. Skipping.

Searching mirecords ...
Searching mirtarbase ...
Searching tarbase ...

Perform KEGG enrichment analysis

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
No genes for CAV down. Skipping...