Gene gain and loss: aCGH ISA CGH

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Probe identifiers Differen t array p latform s for CGH m easurem en ts (BACs, cDNA clon es an d oligon u cleotid es for array sp ots) Users m u st collect an d keep u p d ated th e ch rom osom al coord in ates of th e p robes ISACGH au tom atically retrieves th em an d p lots th e h ybrid iz ation valu es over th e corresp on d in g p osition s in ch rom osom es. Differen t IDs can be u p load ed (En sem bl Id s, accession , Un igen e, HUGO, RefSeq, Affy, BAC n am es...) Ch r1:203465273- 2034 8412 User- d efin ed in form ation on ch rom osom al coord in ates can altern atively be su p p lied to th e p rogram
Genomic copy num ber es tim ation Sm oothing: variation of th e Ad ap tive Weigh ts Sm ooth in g m eth od im p lem en ted in th e p rogram GLAD. Binary s egm entation: ch ecks wh eth er every sin gle p oin t in th e d ata set is a breakp oin t in an iterative way. It u ses a p erm u tation d istribu tion to test for m ean d ifferen ces between grou p s d rawin g robu st in feren ces th at d o n ot rely u p on an y m od el of th e d ata Regres s ion: u ses som e ch aracteristics of lin ear regression of in ten sity m easu re on p osition alon g th e gen om e. Su ch a regression lin e h as slop e close to z ero wh en fitted in region s with h om ogen eou s in ten sity levels bu t th e slop e d iffers form z ero wh en in ten sity m easures on th e left- h an d sid e are h igh er or lower th an in ten sity m easu res in th e righ t- h an d sid e. Given th e p oin ts of in ten sity m easu rem en ts ord ered by th eir p osition in th e ch rom osom e, ou r p roced u re fits a regression lin e for each N con secu tive p oin ts. Th u s a vector of slop es equ ivalen t in som e way to a d erived cu rve of th e origin al d ata is obtain ed . t- test is u sed to to id en tify th e slop e- p eaks th at are big en ou gh to in d icate a break- p oin t in th e in ten sity levels. Is ow indow : tries to id en tify bord ers between region s with a sign ifican t ch an ge in th e valu es of in ten sity of h ybrid iz ation . Given th e in ten sity m easu rem en t p oin ts from th e array ord ered by th eir p osition in th e ch rom osom e, a first step fin d s th ose th at are good can d id ates of bein g su ch bord ers. Rou gh ly sp eakin g, a p oin t will be a good can d id ate if th e p - valu e of a t- test com p arin g som e close p oin ts located at its left an d righ t n eigh borh ood s is low en ou gh . Th e bin ary segm en tation m eth od u ses th e global d istribu tion of th e d ataset wh ile th e oth ers are m ore based on th e local d istribu tion s of th e p oin ts.
Page 1 and 2: Gene gain and los s : aCGH ISA CGH
Page 3 and 4: CNV/ CNP Cop y n u m ber variation
Page 5 and 6: 1. Clon es to cover a gen om ic reg
Page 7 and 8: Array CGH Adv antage ● An alysis
Page 9 and 10: ISA CGH ISACGH allows visualiz in g
Page 11: General outline INPUT: gen e exp re
Page 15 and 16: Plotting data and copy num ber es t
Page 17 and 18: Minim al com m on regions w ith con
Page 19 and 20: Functional annotation of altered co
Page 21 and 22: An exam ple
Page 23 and 24: 2. CGH array data Ejem plo
Page 25 and 26: 4. Gender labels (optional) Ejem pl
Page 27 and 28: 6. Gene expression data Ejem plo
Page 29 and 30: 8. Scale value (optional) Ejem plo
Page 31 and 32: 9. Reference lines (optional) Ejem
Page 33 and 34: Ejem plo 10. If you have replicates
Page 35 and 36: Ejem plo 11. Choose the representat
Page 37 and 38: Ejem plo 13. Download data form reg
Page 39 and 40: Ejem plo 15. Zoom y functional anal
Page 41 and 42: Ejem plo 15. Zoom y functional anal
Page 43 and 44: http://gepas.bioinfo.cipf.es/cgib

Gene gain and loss: aCGH ISA CGH

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