Recent changes to MAP

MAP modified by Mi-kyoung Seo

Mi-kyoung Seo — Mon, 19 Jun 2023 15:25:18 -0000

--- v14
+++ v15
@@ -41,6 +41,7 @@
 * Set the folder where the output file will be created.

 >testP = "/path/to/test"
+>expData = "/path/to/expression.txt"
 >runMAP(expData, testP)

 A description of the function can be found by entering :

MAP modified by Mi-kyoung Seo

Mi-kyoung Seo — Mon, 19 Jun 2023 15:24:35 -0000

--- v13
+++ v14
@@ -35,8 +35,7 @@
 DOCK5  TYMS    HPSE    ASPHD2  AGR2    GFI1    RPL22L1 RAB27B  GNLY    DUSP4


->data(expData) # example RNA-seq expression data (eg. log2(RSEM+1))
-
+>expData # RNA-seq expression data (eg. log2(RSEM+1)) file ("/path/to/expression.txt") 


 * Set the folder where the output file will be created.

MAP modified by Mi-kyoung Seo

Mi-kyoung Seo — Sat, 12 Mar 2022 17:59:04 -0000

--- v12
+++ v13
@@ -27,7 +27,7 @@


 The Input should be a log2 transformed expression matrix.
-You need expression data for all genes that contain a list of 31 genes.
+You need expression data for all genes of whole transcriptome data that contain a list of 31 genes.

 >data(marker) # MAP signaure for MSI, list of 31 genes used in MAPgene model
 >>LY6G6D   CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43

MAP modified by Mi-kyoung Seo

Mi-kyoung Seo — Fri, 07 Feb 2020 18:11:25 -0000

--- v11
+++ v12
@@ -30,7 +30,7 @@
 You need expression data for all genes that contain a list of 31 genes.

 >data(marker) # MAP signaure for MSI, list of 31 genes used in MAPgene model
-**LY6G6D   CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43
+>>LY6G6D   CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43
 PRR15  ATP9A   H2AFJ   FARP1   TCF7    MAPRE3  ZMYND8  DDX27   TGFBR2  PIWIL4  FECH
 DOCK5  TYMS    HPSE    ASPHD2  AGR2    GFI1    RPL22L1 RAB27B  GNLY    DUSP4

MAP modified by Mi-kyoung Seo

Mi-kyoung Seo — Fri, 07 Feb 2020 18:10:50 -0000

--- v10
+++ v11
@@ -30,11 +30,13 @@
 You need expression data for all genes that contain a list of 31 genes.

 >data(marker) # MAP signaure for MSI, list of 31 genes used in MAPgene model
->>LY6G6D   CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43
+**LY6G6D   CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43
 PRR15  ATP9A   H2AFJ   FARP1   TCF7    MAPRE3  ZMYND8  DDX27   TGFBR2  PIWIL4  FECH
 DOCK5  TYMS    HPSE    ASPHD2  AGR2    GFI1    RPL22L1 RAB27B  GNLY    DUSP4

+
 >data(expData) # example RNA-seq expression data (eg. log2(RSEM+1))
+


 * Set the folder where the output file will be created.

MAP modified by Mi-kyoung Seo

Mi-kyoung Seo — Fri, 07 Feb 2020 18:10:11 -0000

--- v9
+++ v10
@@ -30,9 +30,9 @@
 You need expression data for all genes that contain a list of 31 genes.

 >data(marker) # MAP signaure for MSI, list of 31 genes used in MAPgene model
-`LY6G6D    CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43
+>>LY6G6D   CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43
 PRR15  ATP9A   H2AFJ   FARP1   TCF7    MAPRE3  ZMYND8  DDX27   TGFBR2  PIWIL4  FECH
-DOCK5  TYMS    HPSE    ASPHD2  AGR2    GFI1    RPL22L1 RAB27B  GNLY    DUSP4`
+DOCK5  TYMS    HPSE    ASPHD2  AGR2    GFI1    RPL22L1 RAB27B  GNLY    DUSP4

 >data(expData) # example RNA-seq expression data (eg. log2(RSEM+1))

MAP modified by Mi-kyoung Seo

Mi-kyoung Seo — Fri, 07 Feb 2020 18:07:28 -0000

--- v8
+++ v9
@@ -30,7 +30,9 @@
 You need expression data for all genes that contain a list of 31 genes.

 >data(marker) # MAP signaure for MSI, list of 31 genes used in MAPgene model
-`LY6G6D    CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43   PRR15   ATP9A   H2AFJ   FARP1   TCF7    MAPRE3  ZMYND8  DDX27   TGFBR2  PIWIL4  FECH    DOCK5   TYMS    HPSE    ASPHD2  AGR2    GFI1    RPL22L1 RAB27B  GNLY    DUSP4`
+`LY6G6D    CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43
+PRR15  ATP9A   H2AFJ   FARP1   TCF7    MAPRE3  ZMYND8  DDX27   TGFBR2  PIWIL4  FECH
+DOCK5  TYMS    HPSE    ASPHD2  AGR2    GFI1    RPL22L1 RAB27B  GNLY    DUSP4`

 >data(expData) # example RNA-seq expression data (eg. log2(RSEM+1))

MAP modified by Mi-kyoung Seo

Mi-kyoung Seo — Fri, 07 Feb 2020 18:06:52 -0000

--- v7
+++ v8
@@ -30,7 +30,7 @@
 You need expression data for all genes that contain a list of 31 genes.

 >data(marker) # MAP signaure for MSI, list of 31 genes used in MAPgene model
-LY6G6D CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43   PRR15   ATP9A   H2AFJ   FARP1   TCF7    MAPRE3  ZMYND8  DDX27   TGFBR2  PIWIL4  FECH    DOCK5   TYMS    HPSE    ASPHD2  AGR2    GFI1    RPL22L1 RAB27B  GNLY    DUSP4
+`LY6G6D    CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43   PRR15   ATP9A   H2AFJ   FARP1   TCF7    MAPRE3  ZMYND8  DDX27   TGFBR2  PIWIL4  FECH    DOCK5   TYMS    HPSE    ASPHD2  AGR2    GFI1    RPL22L1 RAB27B  GNLY    DUSP4`

 >data(expData) # example RNA-seq expression data (eg. log2(RSEM+1))

Home modified by Mi-kyoung Seo

Mi-kyoung Seo — Fri, 07 Feb 2020 18:04:19 -0000

--- v6
+++ v7
@@ -6,9 +6,9 @@

 ----------
-outstanding features of MAP
+MAP overview
 ------------------------------------------
-
+We present a transcriptomic data-based, absolute, single sample predictor (MAP) that integrates profiles on molecular mechanisms, cancer signatures, immune signatures, and tumor microenvironments (TME) to predict MSI status. To do so, we used 466 samples from The Cancer Genome Atlas and validated the predictive power of the MAP, with 96% accuracy, using an additional 1118 samples, including 250 MSI tumors.

 ----------
 How to install

Home modified by Mi-kyoung Seo

Mi-kyoung Seo — Fri, 07 Feb 2020 18:00:36 -0000

--- v5
+++ v6
@@ -27,9 +27,10 @@

 The Input should be a log2 transformed expression matrix.
-You need expression data for all genes that contain a list of 13 genes.
+You need expression data for all genes that contain a list of 31 genes.

->data(marker) # MAP signaure for MSI, list of 13 genes used in MAPgene model
+>data(marker) # MAP signaure for MSI, list of 31 genes used in MAPgene model
+LY6G6D CYP2W1  TNNC2   CTTNBP2 NKD1    CAB39L  MLH1    EPM2AIP1    SHROOM4 RNF43   PRR15   ATP9A   H2AFJ   FARP1   TCF7    MAPRE3  ZMYND8  DDX27   TGFBR2  PIWIL4  FECH    DOCK5   TYMS    HPSE    ASPHD2  AGR2    GFI1    RPL22L1 RAB27B  GNLY    DUSP4

 >data(expData) # example RNA-seq expression data (eg. log2(RSEM+1))