MutMix: Mutation Association with miRNA Expression in cancers
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MutMix
Other Tissue
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma

FFPE Pilot Phase II

Mesothelioma

Pheochromocytoma and Paraganglioma

Sarcoma

Thymoma
Prostate
Prostate Adenocarcinoma
Testis
Testicular Germ Cell Tumors
Adrenal Gland
Adrenocortical Carcinoma
Cervix
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma

Ovarian Serous Cystadenocarcinoma

Uterine Corpus Endometrial Carcinoma

Uterine Carcinosarcoma
Intestine
Colon Adenocarcinoma

Rectum Adenocarcinoma
Bladder
Bladder Urothelial Carcinoma
Stomach
Stomach Adenocarcinoma
Kidney
Kidney Chromophobe

Kidney Renal Clear Cell Carcinoma

Kidney Renal Papillary Cell Carcinoma
Bile Ducts
Cholangiocarcinoma
Skin
Skin Cutaneous Melanoma
Pancreas
Pancreatic Adenocarcinoma
Mthyroid
Thyroid Carcinoma
Blood
Acute Myeloid Leukemia
Lung
Lung Adenocarcinoma

Lung Squamous Cell Carcinoma
Breast
Breast Invasive Carcinoma
Liver
Liver Hepatocellular Carcinoma
Brain
Brain Lower Grade Glioma
Esophagus
Esophageal Carcinoma
Eye
Uveal Melanoma
Head and Neck
Head and Neck Squamous Cell Carcinoma

Cancer List:
Select the cancers from which the mutation-expression associations were inferred. You can select up to 6 cancers by clicking an item in the list and repeat the process. Cancers can also be selected by clicking on the organ icons on the human figure on the left. The selected cancers appear in the Selected cancers area.


Selected cancer Types:

  • Adrenocortical Carcinoma (ACC)×
  • Bladder Urothelial Carcinoma (BLCA)×
  • Breast Invasive Carcinoma (BRCA)×
  • Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC)×
  • Cholangiocarcinoma (CHOL)×
  • Colon Adenocarcinoma (COAD)×
  • Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (DLBC)×
  • Esophageal Carcinoma (ESCA)×
  • FFPE Pilot Phase II (FPPP)×
  • Head and Neck Squamous Cell Carcinoma (HNSC)×
  • Kidney Chromophobe (KICH)×
  • Kidney Renal Clear Cell Carcinoma (KIRC)×
  • Kidney Renal Papillary Cell Carcinoma (KIRP)×
  • Acute Myeloid Leukemia (LAML)×
  • Brain Lower Grade Glioma (LGG)×
  • Liver Hepatocellular Carcinoma (LIHC)×
  • Lung Adenocarcinoma (LUAD)×
  • Lung Squamous Cell Carcinoma (LUSC)×
  • Mesothelioma (MESO)×
  • Ovarian Serous Cystadenocarcinoma (OV)×
  • Pancreatic Adenocarcinoma (PAAD)×
  • Pheochromocytoma and Paraganglioma (PCPG)×
  • Prostate Adenocarcinoma (PRAD)×
  • Rectum Adenocarcinoma (READ)×
  • Sarcoma (SARC)×
  • Skin Cutaneous Melanoma (SKCM)×
  • Stomach Adenocarcinoma (STAD)×
  • Testicular Germ Cell Tumors (TGCT)×
  • Thyroid Carcinoma (THCA)×
  • Thymoma (THYM)×
  • Uterine Corpus Endometrial Carcinoma (UCEC)×
  • Uterine Carcinosarcoma (UCS)×
  • Uveal Melanoma (UVM)×


Paste or upload gene/Isoform
Type or paste one or multiple gene/miRNA names in the text box. The total number is limited to 200. Check the corresponding entity type (mRNA/miRNA) in the Parameters section on the right. When miRNAs are inputted, the user is performing a reverse query of the associations, and thus the output contents may be different from the default forward query.
 Pre-curated gene sets
Paste gene/Isoform
 OR
Upload a file
 Parameters
 cancer-related pathways
A total of 379 cellular pathways compiled from PID, PAHTHER, and INOH are pre-curated here (10.1371/journal.pcbi.1008976). Users can select one pathway, which is converted to a gene set. Type in key words and the related pathways will show up for selection.
Example
  		 mRNA 
Input is mRNA, mutation-miRNA association will be searched based on mRNA

 Isoform
Input is miRNA, mutation-miRNA association will be searched based on miRNA


 Enable Fuzzy Match
Fuzzy search allows partial matching from the left of the mRNA/miRNA names. For examle, TP53 will match all all genes that have 'TP53' in its gene symbol

Association
Mutation
Network
Disease
Survival analysis
Association between miRNA expression and cancer patient survival. Multiple miRNAs’ expression is summarized with the CGES method (10.1080/15476286.2019.1679585). Users can choose between Disease-Specific Survival (DSS) and Overall Survival (OS).




 Kaplan-Meier plot 		 TF
Indicate if the mRNA gene is a Transcription Factor (TFome of ~1.5k genes from 10.1038/s41587-020-0742-6).
 SomamiR
Somatic mutations altering microRNA regulations, as curated in SomamiR DB 2.0.
  miRNA-mRNA
Associations between miRNA and mRNA.
  miRNA-Disease
Associations between miRNA and disease.
 RBP
Indicate if the mRNA gene is a RNA-binding protein (RBP human census 2014, 10.1038/nrg3813)
  Patient mutation oncoprint
OncoPrint is a heatmap showing mutation situations of multiple genes across a patient cohort.
 TransmiR curation
Occurrence in TransmiR v2.0, a database on TF-miRNA regulations.
  miRNA conservation
Conservation level classified by TargetScan. Values take from (-1, 0, 1, 2), mapping to others, poorly conserved, conserved, and broadly conserved.
  Gene mutation ideogram
An ideogram showing gene body structure with mutations marked out.
  Per-gene intersection
Intersection of associations across multiple cancers per each gene.
  Per-cancer intersection
Intersection of associations across multiple genes per each cancer.
  Somatic Motif
Annotation on altered binding sequences: miRNA seed, miRNA-mRNA 5'UTR binding sequence, and RNA binding protein sequence
  Pathways
Indicate if the gene and miRNA belong to the same Pathway.

paste a gene list Upload a file with genes choose a pathway with genes
Please do not submit repeatedly