Help Page of CancerTSP |
| CancerTSP (Thyroid cancer stage prediction) is a web-bench developed for predicting Early and Late stage of Thyroid cell carcinoma (THCA) patients using gene expression data derived from RNA-seq experiments in the form of (FPKM) values. The user can also analyze data regarding expression of a gene in early and late stage of THCA for any genes included in TCGA analysis. The models used in this study were trained on TCGA genomics data for cancer patients of 519 cancer patients. We are able to discriminate between early and late stage patients with accuracy of 74.51% with AUROC of 0.75 on validation dataset. |
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PREDICTION | |||||||||||||||||||||||||||||||||||
| Predict Early vs Late samples using all transcripts | |||||||||||||||||||||||||||||||||||
| This tool allows the users to submit FPKM values of RNA transcripts and predict if the cancer patient has Early Stage cancer or Late Stage cancer using RNA expression data of 36 RNA transcripts, resulting from classification analysis of RNA-seq data of THCA(or PTC) from TCGA data. This method requires FPKM values of 36 RNA transcripts in each patient to predict whether it’s in early or late stage of cancer. The first column is RNA transcript and in second column expression of corresponding RNA transcript in a particular number of patients. | |||||||||||||||||||||||||||||||||||
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The result Page shows like the following. The result Page provides the output predicting if a sample is Early or Late stage Thyroid Carcinoma using 78 transcripts dataset with their corresponding score. | |||||||||||||||||||||||||||||||||||
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 | Predict Early vs Late samples using protein coding transcripts |
This tool allows the users to submit FPKM values of protein coding RNA transcripts and predict if the cancer patient has Early Stage cancer or Late Stage cancer using RNA expression data of 37 protein coding RNA transcripts, resulting from threshold based analysis of RNA-seq data of THCA (or PTC) from TCGA data. This method requires FPKM values of 37 protein coding RNA transcripts in each patient to predict whether it’s in early or late stage of cancer. The first column is RNA and in second column expression of corresponding RNA in a particular number of patients.
| |  The result Page shows like the following. The result Page provides the output predicting if a sample is Early or Late stage Thyroid Carcinoma using 37 transcripts dataset with their corresponding score.  | Predict Normal vs Cancer samples using gene expression data |
This tool allows the users to submit FPKM values of mRNA and predict the disease's condition using mRNA expression data of 5 signature mRNAs, resulting from analysis of mRNA-seq data of PTC (or THCA) from TCGA dataset from GDC Data portal . This method requires FPKM values of 5 mRNA in each patient to predict whether subject have normal or cancerous status. The first column is mRNA and in second column expression of corresponding mRNA in terms of FPKM value in a particular number of patients.
| |  The result Page shows like the following. The result Page provides the output predicting if a sample is normal or in Cancer of Thyroid Carcinoma using 5 gene dataset with their corresponding score.  | Predict Normal vs Early and Late stage samples (Multiclass Classification) using gene expression data |
This tool allows the users to submit FPKM values of RNA transcripts and predict if the cancer patient normal, Early Stage cancer or Late Stage cancer using RNA expression data of 107 RNA transcripts, resulting from multiclass analysis of RNA-seq data of THCA (or PTC) from TCGA data. This method requires FPKM values of 107 RNA transcripts in each patient to predict whether it’s normal, early stage or late stage of cancer. The first column is RNA transcript and in second column expression of corresponding RNA transcript in a particular number of patients.
| |  The result Page shows like the following. The result Page provides the output predicting if a sample is normal or in Early stage or Late stage of Thyroid Carcinoma using 212 gene dataset with their corresponding score.  | ANALYSISGene-wise Analysis |
This tool allows the analysis of cancer genomics data for subjects in terms of FPKM value. User can submit the FPKM value of RNA transcripts and analyze whether the normalized score of the patient/subject is above or below the given threshold. If RNA is overexpressed in early stage, and score of patient is above threshold then its chance that the patient is in early stage. Thus, the user can see what is the expression status of each RNA transcript, which can point towards whether the patient is in early or late stage of cancer.
| |  > | This tool allows the users to submit FPKM values of RNA transcripts and assess the status of each gene. This module gives threshold which can give assessment whether a sample is in early or late stage. If gene is overexpressed in late stage i.e. its average normalized expression is less in early stage as compared to the late stage in training data and for a given sample, has normalized expression more than the threshold, then we classify that sample as late stage otherwise as early stage. In order to optimize the threshold to achieve best performance, iteration technique was used; where threshold was increased or decreased systematically for a range of normalized expression values across all the samples for a particular gene. This module also gives ROC value calculated using threshold based method. It also gives mean expression of this gene in early and late stage of PTC (or THCA) samples in TCGA. It also provides FPKM value converted to Zscore. The blue color represents that score of this gene is in the range of threshold that it belongs to early stage and red color denotes that it is the range due to which it belongs to late stage.  | |