1. TCGA Cancer Type Abbreviations

  2. Sr. No. Abbreviation Cancer Type
    1 TCGA-ACC Adrenocortical carcinoma
    2 TCGA-BLCA Bladder urothelial carcinoma
    3 TCGA-BRCA Breast invasive carcinoma
    4 TCGA-CESC Cervical squamous cell carcinoma and endocervical adenocarcinoma
    5 TCGA-CHOL Cholangiocarcinoma
    6 TCGA-COAD Colon adenocarcinoma
    7 TCGA-COADREAD Colorectal adenocarcinoma
    8 TCGA-DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
    9 TCGA-ESCA Esophageal carcinoma
    10 TCGA-GBM Glioblastoma multiforme
    11 TCGA-GBMLGG Glioma
    12 TCGA-HNSC Head and Neck squamous cell carcinoma
    13 TCGA-KICH Kidney Chromophobe
    14 TCGA-KIPAN Pan-kidney cohort(KICH+KIRC+KIRP)
    15 TCGA-KIRC Kidney renal clear cell carcinoma
    16 TCGA-KIRP Kidney renal papillary cell carcinoma
    17 TCGA-LGG Brain Lower Grade Glioma
    18 TCGA-LIHC Liver hepatocellular carcinoma
    19 TCGA-LUAD Lung adenocarcinoma
    20 TCGA-LUSC Lung squamous cell carcinoma
    21 TCGA-MESO Mesothelioma
    22 TCGA-OV Ovarian serous cystadenocarcinoma
    23 TCGA-PAAD Pancreatic adenocarcinoma
    24 TCGA-PCPG Pheochromocytoma and Paraganglioma
    25 TCGA-PRAD Prostate adenocarcinoma
    26 TCGA-READ Rectum adenocarcinoma
    27 TCGA-SARC Sarcoma
    28 TCGA-SKCM Skin Cutaneous Melanoma
    29 TCGA-STAD Stomach adenocarcinoma
    30 TCGA-TGCT Testicular Germ Cell Tumors
    31 TCGA-THCA Thyroid carcinoma
    32 TCGA-THYM Thymoma
    33 TCGA-UCEC Uterine Corpus Endometrial Carcinoma
    34 TCGA-UCS Uterine Carcinosarcoma
    35 TCGA-UVM Uveal Melanoma

  3. miRNA Clusters
  4. Generally, a miRNA cluster consists of two or more miRNAs residing neighborly on the same strand. miRNAs in a cluster are not separated by a transcription unit and transcribed in the same orientation. The miRNAs reported from the clusters are co-expressed and jointly regulate functionally associated genes. Some studies have reported that clustered miRNAs are transcribed as poly-cistrons and have similar expression patterns.The intergenomic distance between two miRNAs is considered to group miRNAs as a cluster. Multiple studies have already demonstrated different distance limits are used by researchers to find clusters. According to the miRbase repository, more than 40% of experimentally validated human miRNA cluster genes have been identified within the 10 kb region.

  5. CmirC
  6. CmirC is a cancer omics database which provides information for recurrent copy number varition (RCNV) colocalized miRNA clusters from 35 TCGA cancer types. Here we are presenting the primary version of CmirC which will be further expanded according to subsequent TCGA data update

    Methdology
  7. Workflow of Data Browsing Modules

  8. Data browsing modules allows user to extensively browse data stored in database with multiple options:


    Diagram1

    Interactive data visualization by CmirC. A. Circos plot illustrating identified RCNA and co-localized miRNA Clusters B. miRNA Cluster and target gene network C. Individual miRNA targets D. Average read per million (RPM) expression of miRNA across TCGA cancer types E. miRNA differential expression (Normal vs Tumor) across the TCGA cancer types F. Top 20 enriched pathways for gene set targetd by miRNA clusters G. Gene set enriched in the cancer network


  9. Genome Browser
  10. Genome browser module is developed to visualize the RCNA and miRNA cluster colocalization across 35 TCGA cancer types. Here user can select particular TCGA cancer type, Chromosome Fragile Site, mature or precurssor form of miRNA and can highlight the clustered miRNAs. By clicking on zoom function user can also see the miRNA name and by clicking on miRNA, on pop up window user can see the information available in database for that particular miRNA.


    GenomeBrowser
  11. Basic Local Alignment Search Tool (BLAST)
  12. BLAST module is developed for performing BLAST search against nucleotide sequence of Clusterd miRNAs. User are requested to submit sequence only in FASTA format. This is a nucleotide to nucleotide search, so BLASTN will be use to perform search.

    blast
  13. miRNA Cluster Details Page

  14. blast
  15. Individual miRNA Details Page

  16. blast