whichModuleShouldIChoose

2020-02-27 251浏览

  • 1.Modules in BioCircos2
  • 2.Modules:• Mutation • SNP • CNV • HEATMAP • LINK • SCATTER • ARC • HISTOGRAM • LINE • CHORD • TEXT • BACKGROUND
  • 3.Mutation:Mutation module displays a bunch of mutation points in a chromosome(or gene, protein,…) based on its position • Datastructure:• The 1 column(protein) is the name of the protein. • The 2 column(chr) is the name of the chromosome. • The 3 column(pos) is the position of the mutation. • The 4 column(strand) is the strand where the mutation from. • The 5 column(CancerTypeNumber) is the number of cancer type in which the mutation can be found. • The 6 column(AA_pos), 7 column(AA_change), 8 column(Consequence) is other information for the mutation. • The 9 column(color) is the color for the mutation • The 10 column(type):Hetero:the mutation is made up of two half circle,Homo:the mutation is made up of a circle. • The 11 column(link) is the website link site for the mutation if you click the mutation(hyperlink is activated)
  • 4.Mutation module looks likebelow:Select gene_EGFR at step1 and upload MutationDetailsExample.txt
  • 5.SNP:SNP module is used to display the SNP density data, GWAS data, etc. Of cour se, other data have similar structure can also be displayed by SNP module. • Datastructure:• The 1 column(chr) is the name of the chromosome. • The 2 column(pos) is the position of the SNP. • The 3 column(value) is the value(density, P-value, etc.) of the SNP. • The 4 column(des) is the description of the SNP.
  • 6.SNP module looks likebelow:Select hg19 at step1 and upload SNPExample.txt
  • 7.CNV:CNV module is used to display the CNV data, etc. Of course, other data have similar structure can also be displayed by CNV module. • Datastructure:• The 1 column(chr) is the name of the chromosome. • The 2 column(start) is the start of the CNV region. • The 3 column(end) is the end of the CNV region. • The 4 column(value) is the copy number of CNV region.
  • 8.CNV module looks likebelow:Select hg19 at step1 and upload CNVExample.txt
  • 9.HEATMAP:HEATMAP module is used to display the Gene expression data, etc. Of course, other data have similar structure can also be displayed by HEATMAP module. • Datastructure:• The 1 column(chr) is the name of the chromosome. • The 2 column(start) is the start of the region. • The 3 column(end) is the end of the region. • The 4 column(name) is the name of the region. • The 5 column(value) is the value of the region.
  • 10.HEATMAP module looks likebelow:Select chr(2L,2R,3L,3R,X,4) at step1 and upload HEATMAPExample.txt
  • 11.LINK:LINK module is used to display the Gene fusions data, Interaction data, SV data etc. Of course, other data have similar structure can also be displayed by LINK module. • Datastructure:• The 1 column(name) is the name of the link. • The 2 column(g1chr) is the chromosome of gene 1. • The 3 column(g1start) is the start of gene 1. • The 4 column(g1end) is the end of gene 1. • The 5 column(g1name) is the name of gene 1. • The 6 column(g2chr) is the chromosome of gene 2. • The 7 column(g2start) is the start of gene 2. • The 8 column(g2end) is the end of gene 2. • The 9 column(g2name) is the name of gene 2.
  • 12.LINK module looks likebelow:Select hg19 at step1 and upload LINKExample.txt
  • 13.SCATTER:SCATTER module is used to display the SNP without value, Genes data, etc. Of co urse, other data have similar structure can also be displayed by SCATTER module. • Datastructure:• The 1 column(chr) is the name of the chromosome. • The 2 column(start) is the start position of the scatter. • The 3 column(end) is the end position of the scatter. • The 4 column(name) is the name of the scatter. • The 5 column(des) is the description of the scatter.
  • 14.SCATTER module looks likebelow:Select hg19 at step1 and upload SCATTERExample.txt
  • 15.ARC:ARC module is used to display the CNV without value, Gene domain, Chromosome band , etc. Of course, other data have similar structure can also be displayed by ARC module. • Datastructure:• The 1 column(chr) is the name of the chromosome. In this example, this field specify the protein name. • The 2 column(start) is the start of the arc. • The 3 column(end) is the end of the arc. • The 4 column(color) is the color of the arc. • The 5 column(des) is the description of the arc. • The 6 column(link) is the website link of the arc.
  • 16.ARC module looks likebelow:Select gene_EGFR at step1 and upload ARCExample.txt
  • 17.HISTOGRAM:HISTOGRAM module is used to display the Gene expression data, etc. Of course, other data have similar structure can also be displayed by HISTOGRAM module. • Datastructure:• The 1 column(chr) is the name of the chromosome. • The 2 column(start) is the start of the region. • The 3 column(end) is the end of the region. • The 4 column(name) is the name of the region. • The 5 column(value) is the value of the region.
  • 18.HISTOGRAM module looks likebelow:Select chr(2L,2R,3L,3R,X,4) at step1 and upload HISTOGRAMExample.txt
  • 19.LINE:LINE module is used to display the Gene expression data, etc. Of course, oth er data have similar structure can also be displayed by LINE module. • Datastructure:• The 1 column(chr) is the name of the chromosome. • The 2 column(pos) is the position of the point. • The 3 column(value) is the value of the point.
  • 20.LINE module looks likebelow:Select hg19 at step1 and upload LINEExample.txt
  • 21.CHORD:CHORD module display the link information between two base sequence like chr omosome, exon, protein, etc. • Datastructure:• The 1 row is a list contains all base sequence name. • The 2 matrix is the relative matrix among all base sequence, the number in matrix is the base number between each 2 proteins. For example, [1,2] and [2,1] means a chord between protein1 and protein2, in which [1,2]=304 5 means the base number in protein1 is 3045 and [2,1]=3214 means the base number in protein2 is 3214.
  • 22.CHORD module looks likebelow:Select hg19 at step1 and upload CHORDExample.txt
  • 23.TEXT:TEXT module is used to display annotation text at specific elements. • Select hg19 at step1 and default settings at step2
  • 24.BACKGROUND:BACKGROUND module is used to display background and axis circles for oth er modules. • Select hg19 at step1 and default settings at step2