Recent changes to mutation_report

mutation_report modified by Keith Ching

Keith Ching — Mon, 20 Feb 2017 20:26:34 -0000

--- v5
+++ v6
@@ -8,3 +8,5 @@
 [example query](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=2&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=mutation_report&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&active_Mutation=3&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=kras&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10) show the mutations found in KRAS.

 Background:  Typically,  a mutation will be identified in a gene that does not match one of the cannonical drivers or tumor suppressors.  These mutations are often ignored.  However, if the sample is very important like a therapy resistant tumor or an exceptional responder to treatment, then every mutation will be analyzed carefully to see how it relates to the biology of the tumor and the treatment.  One way to gather support for a mutation's significance is to see if that mutation has ever been observed before in any dataset.  Certain amino acid positions are critical to a protein's function and mutations falling on the same position may indicate an important residue.  Certain mutations are also more prevalent in tumors from specific tissues.  It can be useful to see where else a specific mutation occurs.  Beware of tumors with mutator phenotypes / MSI tumors that contain > 1000 somatic mutations as these can be passengers. (Check using MUT-COUNT)
+
+dev: querying for multiple genes in the HUGO box and checking dataset frequency box will instead generate a table of source x gene containing the percentage of sample containing a mutation in the given gene.

mutation_report modified by Keith Ching

Keith Ching — Tue, 01 Mar 2016 22:01:57 -0000

--- v4
+++ v5
@@ -7,4 +7,4 @@

 [example query](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=2&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=mutation_report&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&active_Mutation=3&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=kras&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10) show the mutations found in KRAS.

-Background:  Typically,  a mutation will be identified in a gene that does not match one of the cannonical drivers or tumor suppressors.  These mutations are often ignored.  However, if the sample is very important like a therapy resistant tumor or an exceptional responder to treatment, then every mutation will be analyzed carefully to see how it relates to the biology of the tumor and the treatment.  One way to gather support for a mutation's significance is to see if that mutation has ever been observed before in any dataset.  Certain amino acid positions are critical to a protein's function and mutations falling on the same position may also indicate an important residue.
+Background:  Typically,  a mutation will be identified in a gene that does not match one of the cannonical drivers or tumor suppressors.  These mutations are often ignored.  However, if the sample is very important like a therapy resistant tumor or an exceptional responder to treatment, then every mutation will be analyzed carefully to see how it relates to the biology of the tumor and the treatment.  One way to gather support for a mutation's significance is to see if that mutation has ever been observed before in any dataset.  Certain amino acid positions are critical to a protein's function and mutations falling on the same position may indicate an important residue.  Certain mutations are also more prevalent in tumors from specific tissues.  It can be useful to see where else a specific mutation occurs.  Beware of tumors with mutator phenotypes / MSI tumors that contain > 1000 somatic mutations as these can be passengers. (Check using MUT-COUNT)

mutation_report modified by Keith Ching

Keith Ching — Tue, 01 Mar 2016 21:55:47 -0000

--- v3
+++ v4
@@ -5,6 +5,6 @@

 Usage: Enter a gene symbol into the HUGO box. press submit.

-[example query](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=2&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=mutation_report&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&active_Mutation=3&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=kras&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)
+[example query](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=2&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=mutation_report&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&active_Mutation=3&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=kras&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10) show the mutations found in KRAS.

-show the mutations found in KRAS.
+Background:  Typically,  a mutation will be identified in a gene that does not match one of the cannonical drivers or tumor suppressors.  These mutations are often ignored.  However, if the sample is very important like a therapy resistant tumor or an exceptional responder to treatment, then every mutation will be analyzed carefully to see how it relates to the biology of the tumor and the treatment.  One way to gather support for a mutation's significance is to see if that mutation has ever been observed before in any dataset.  Certain amino acid positions are critical to a protein's function and mutations falling on the same position may also indicate an important residue.

mutation_report modified by Keith Ching

Keith Ching — Tue, 01 Mar 2016 21:38:49 -0000

--- v2
+++ v3
@@ -1,7 +1,9 @@
+[Instructions]
 mutation_report

 Show the diversity and number of mutations found database wide in the selected gene.  One purpose of the report is to determine if a given mutation, or mutation position is often mutated. The output is a table of datasource, mutation, position and number of times found in the dataset.  Graphical versions are implemented in [Oasis Genomics](http://oasis-genomics.org/) and [cBio Portal](http://www.cbioportal.org/).

+Usage: Enter a gene symbol into the HUGO box. press submit.

 [example query](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=2&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=mutation_report&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&active_Mutation=3&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=kras&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

mutation_report modified by Keith Ching

Keith Ching — Tue, 01 Mar 2016 21:34:08 -0000

--- v1
+++ v2
@@ -1 +1,8 @@
 mutation_report
+
+Show the diversity and number of mutations found database wide in the selected gene.  One purpose of the report is to determine if a given mutation, or mutation position is often mutated. The output is a table of datasource, mutation, position and number of times found in the dataset.  Graphical versions are implemented in [Oasis Genomics](http://oasis-genomics.org/) and [cBio Portal](http://www.cbioportal.org/).
+
+
+[example query](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=2&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=mutation_report&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&active_Mutation=3&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=kras&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)
+
+show the mutations found in KRAS.

mutation_report modified by Keith Ching

Keith Ching — Wed, 14 Oct 2015 00:00:16 -0000

mutation_report