Pathway Ranking Tool

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Pathway Ranking Tool Dimitri Kosturos Linda Tsai SoCalBSI, 8/21/2003

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Pathway Ranking Tool. Dimitri Kosturos Linda Tsai SoCalBSI, 8/21/2003. Project Overview. Project Overview. BioDiscovery, Inc. at Marina del Rey Analyzing microarray data on pathway level instead of individual gene level Methods: -Enrichment Analysis -Permutational Statistics - PowerPoint PPT Presentation

Transcript of Pathway Ranking Tool

  • Pathway Ranking ToolDimitri Kosturos Linda TsaiSoCalBSI, 8/21/2003

  • Project OverviewBioDiscovery, Inc. at Marina del ReyAnalyzing microarray data on pathway level instead of individual gene levelMethods:-Enrichment Analysis-Permutational Statistics-S. Metric-Multivariate test

    Project Overview

  • Validation of statistical methods2 data sets: Brain Tumor, Interferon-gamma.Sources of annotation: BioCarta, Kegg, Gene Ontology.Project Overview, cont.

  • phenotypemicroarrayalgorithmpathwayProject Flowchart

    Dimitri,(Computer Scientist)

    Linda(biologist)

  • GeneSight is a data analysis softwareFeature:-Statistical significance testing-Multiple Data Visualizations -Automated gene annotation-Complete result reports-Pathway analysis (?)Research and Development in GeneSight

  • Glioblastoma multiforme(GBM) is the most malignant of the glial tumors, classified as grade IV.

    Many brain tumors are currently incurable.Average survival time: 1 yearBiology of Brain Tumor

  • Oncogenes: promote normal cell growth Tumor suppressor genes: retard cell growth http://www.med.harvard.edu/publications/On_The_Brain/Volume4/Number2/SP95Awry.htmlBad Genes Foment Trouble

  • Interferon is a class of cytokines that mediate antiviral, antiproliferative, antitumor activites, etc.IFN gamma is produced by T lymphocytes in response to mitogens or to antigens. IFNs bind to their receptors and initiate JAK-STAT signaling cascade.Biology of Interferon

  • http://www.grt.kyushu-u.ac.jp/eny-doc/pathway/ifn_gamma.htmlBiology of Interferon, cont.

  • Grouping related genes together into pathways(A)BioCartaEx: p53 Signaling Pathway(B)KEGGEx:Citrate cycle (TCA cycle)Grouping genes into structured, controlled vocabularies (ontologies) Gene Ontology-Biological Process. Ex: angiogenesis, apoptosis-Molecular Function. Ex: DNA binding activity-Cellular Component.Ex: nucleus, mitochondria

    Gene Annotations

  • Traditional method of ranking gene pathwaysSteps:1. Mann-Whitney Test: obtain list of probe sets that satisfy a certain p-value.2. Cluster analysis: see how many of listed probe occur in a cluster (pathway).

    Example:Original data: 12,625 genes. Select genes p-value narrow to 927 genes.2.Cluster those 927 genes into clusters.

  • Mann-Whitney Test, Denovo Glioblastoma p

  • How Affy. Microarray Chips Workhttp://www.ucl.ac.uk/oncology/MicroCore/HTML_resource/Norm_Affy1.htmBest results: Genes hybridize perfectly with Perfect Match, and not at all with Mismatch. PM: Perfect Match MM: Mismatch

  • Example of GeneSight PlotDataTheoretical Tumor Expression Levels (Log Transformed)Notice column replicates, Probe Set replicates.

  • Given Data SetsGiven two data sets: Brain Tumor, IFN-Brain Tumor Data Set has 5+ tumor types,however, only 2 Tumor types were used (Denovo Glioblastoma, Progressive Glioblastoma)IFN- Data Set: the entire data set was used.

  • What and why?Goal: write a prototype extension to GeneSight that uses permutational statistics to develop a custom distribution for a given Microarray data set.Overall significance: the software provides a list of (potentially) significant pathways that enables researchers to focus their work.

  • What is permutational statistics?Choose different Control and Experiment groupings (permute).

    By iterating through an adequate number of permutations, we can determine if a pathway is likely to be significant (p-value).

    (In this context.)

  • Permutational Stats.There are two versions of the S. Metric currently implemented.S. Metric I =S. Metric II =M = Number of Genes flagged as significantTotal = Total number of Genes in the Pathway

  • (Layman's) How Statistics WorksDataStatisticP-ValuePermute HereS. Metric I, IIAfter all permutations are done, calculate the p-Value

  • AlgorithmTake at least 10,000 unique permutations. A unique permutation is determined by a Permute class. For each condition For each permutation For each gene Calc. Mean diff. Calc. T-stat End For For each pathway store the statistic End for End for calcPvalue(stored statistic) End For pValue

  • LimitationsComputational Power (Memory, CPU)Required number of replicates (8,8)

  • Output of result

  • Validation of pathway analysisMethod 1Problem: lack of insignificant pathways????

    Sheet1

    Computer algorithm classified as significant pathwaysComputer algorithm classified as insignificant pathways

    Linda's Selection of significant pathwaysTrue PositiveFalse Negative

    Linda's Selection of insignificant pathwaysFalse PositiveTrue Negative

    Sheet2

    Sheet3

  • Validation of pathway analysisMethod 2Comparision of Prediction Methods024681012141616111621263136414651566166717681869196# of Pathways in BioCarta sorted by P-value# of identified significant pathways

    Best algorithm

    Random

    Worst

  • ResultBrain Tumor-BioCarta

    Chart1

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    # of pathways in BioCarta sorted by P-value

    # of sig. identified pathways

    D. glioblastoma

    bioCarta-D. Glioblastoma

    insig. SMIinsig. SMIIinsig DG0.001insig DG0.01SMISMIIDG0.001DG0.01

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    bioCarta-D. Glioblastoma

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    insig. SMII

    insig DG0.001

    insig DG0.01

    Number of Pathways in BioCarta

    Number of Identified pathways

    D. glioblastoma-BioCarta Insignificant

    KEGG-D.Glioblastoma

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    # of identified pathways

    D. glioblastoma

    BP-D. Glioblastoma

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    BP-D. Glioblastoma

    0000

    0000

    0000

    0000

    0000

    0000

    0000

    0000

    0000

    0000

    0000

    0000

    0000

    0000

    0000

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    1600

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    2600

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    3600

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    SMI

    insig. SMII

    DG0.001

    DG0.01

    # of pathways in KEGG

    # of identified pathways

    D. Glioblastoma sort2

    CC-D. Glioblastoma

    SMISMIIDG0.001DG0.01insig SMIinsig SMIIinsig DG0.001insig DG0.01

    00000010

    00000010

    00000010

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    SMI

    SMII

    DG0.001

    DG0.01

    #of terms in biological process

    # of terms identified

    D. Glioblastoma-BP(GO)

    MF-D. Glioblastoma

    0000

    0000

    0000

    0000

    0000

    0100

    0100

    0100

    0100

    0100

    0100

    0100

    0100

    0100

    1100

    2100

    2100

    2100

    2100

    2100

    2100

    2100

    2100

    3100

    3100

    4100

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    4100

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    4100

    4100

    4100

    4100

    4100

    4100

    4200

    5300

    5300

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    5900

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    5900

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    51000

    51000

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    51000

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    51000

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    51000

    51000

    51000

    51000

    51000

    61000

    61100

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    81100

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    81100

    91100

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    91200

    91200

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    91200

    101200

    101200

    101200

    101200

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    101200

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    101200

    111200

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    141200

    141300

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    201900

    202000

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    202200

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    202800

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    202900

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    203000

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    213000

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    223000

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    223000

    233000

    233000

    233100

    233200

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    304100

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    304200

    304300

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    314600

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    524900

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    525000

    525100

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    525100

    525100

    525200

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    535300

    535300

    insig SMI

    insig SMII

    insig DG0.001

    insig DG0.01

    #of terms in biological process

    # of terms identified

    D. Glioblastoma- insignificant BP(GO)

    BioCarta-P. Glioblastoma

    SM-ISMIIDG0.001DG0.01

    000

    000

    000

    000

    000

    000

    000

    001

    011

    021

    031

    041

    042

    043

    043

    043

    053

    053

    053

    053

    053

    053

    053

    053

    053

    053

    053

    053

    063

    063

    073

    074

    074

    074

    074

    074

    074

    074

    074

    075

    075

    076

    076

    076

    076

    076

    176

    277

    377

    477

    577

    677

    777

    877

    977

    1077

    1178

    1278

    1378

    1478

    1578

    1678

    1778

    1778

    1788

    1788

    1798

    1798

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    1798

    17108

    17108

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    17108

    17108

    17108

    17118

    17118

    17118

    17118

    17118

    17118

    17118

    17118

    17128

    17128

    17129

    17129

    17129

    17129

    17129

    17129

    17139

    17139

    17139

    17139

    17139

    17149

    17149

    17159

    17159

    17159

    17159

    17159

    171610

    171710

    171710

    171710

    171710

    171710

    171710

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    171710

    171710

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    181821

    181821

    181821

    181821

    181821

    181821

    181821

    191921

    202021

    212121

    BioCarta-P. Glioblastoma

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    100

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    1700

    1700

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    1800

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    1800

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    2100

    SMII

    DG0.001

    DG0.01

    # of terms in CC

    # of identified terms

    D. glioblastoma-CC (GO)

    KEGG-P.Glioblastoma

    SM-I(sort2)SMIIDG0.001DG0.01

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    000

    010

    010

    010

    010

    010

    010

    010

    010

    010

    020

    020

    020

    020

    020

    020

    020

    020

    020

    020

    020

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    020

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    021

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    032

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    032

    032

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    035

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    035

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    035

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    035

    035

    035

    035

    035

    036

    036

    036

    036

    036

    036

    036

    036

    036

    036

    036

    036

    037

    038

    038

    038

    038

    038

    038

    038

    038

    038

    038

    038

    038

    038

    038

    048

    048

    048

    048

    058

    058

    058

    058

    058

    058

    058

    058

    058

    058

    058

    058

    158

    258

    358

    458

    558

    658

    758

    858

    958

    1058

    1158

    1258

    1358

    1458

    1558

    1658

    1758

    1858

    1958

    2058

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    2058

    2058

    2068

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    2068

    2068

    2068

    2068

    2068

    2068

    2068

    2078

    2078

    2078

    2088

    2088

    2088

    2088

    2098

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    23108

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    23108

    23108

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    24108

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    24108

    24118

    24118

    24118

    24118

    24118

    24118

    24118

    24118

    24118

    24118

    24118

    24118

    24118

    25118

    25128

    25128

    25128

    25128

    25138

    25138

    25149

    251410

    251510

    261610

    261610

    261610

    261610

    261610

    261610

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    272117

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    272217

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