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Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
Pathway AnalysisKarl Brand, June 2012
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
overview
1. goal
2. annotation
3. tools (various approaches, pros & cons)
4. underlying statistics (Fisher’s exact test)
5. in use (DAVID)
6. to summarise
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
goal
To understand genomics results
&/or
Translate genomics data into knowledge
&/or“…for gaining insight into the underlying biology ofdifferentially expressed genes and proteins, as it reducescomplexity and has increased explanatory power”1
1Khatri et al., 2012
To facilitate generating a testable hypothesis
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
tools
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at~
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
You have :Applied methods to identify differentially regulated biological entities (BEs), e.g. p < 0.05 with fold change greater than 1.5
What now?You could pass this list to your chosen pathway analysis tool, but first…
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
annotation
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
Synonyms AcronymsHomonyms
Different names for the same biological entity
Same name for different biological entities
Reduced words representing biological entities
5418 genes with synonyms (38% of total)
PAP, alias for:● PAP (Pancreatitis-associated protein)● MRPS30 (Mitochond ribosomal prot 30S)● PAPOLA (Poly(A) polymerase alpha)
SCT stands for:● Stem cell transplant● Secretin● Salmon calcitonin
annotation: a modern problem
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
Dutch printed map 1600’s Discoveries of Willem Jansz: 1606 is the first recorded European
discovery of Australia (New Holland) at Cape York Peninsula
annotation
Slide by A. Stubbs
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
And now! Post Genome view of the world
annotation
Slide by A. Stubbs
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
These changes reflect new information or analysis The frequency of the changes can
be problematicAttempts made to ‘hide’ this
IDs merged/ deleted/ temporarily un-mapped on the genome sequence
Even common concepts such as Genes Boundaries move, TF Binding
Sites discovered
Database (and their IDs) Change Over Time…Database (and their IDs) Change Over Time…
The Shifting Sands of Databasesand Genome builds…
“M. Moorhouse”
annotation
Slide by M. Moorhouse
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
annotation
Khatri et al., 2012
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
annotation
Khatri et al., 2012
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
annotation
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
annotation
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
tools
You have :Applied methods to identify differentially expressed gene’s* (DEGs), e.g. p < 0.05 with fold change greater than 1.5
What now?
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
You could pass this list to your chosen pathway analysis tool, but first… ensure you have mapped your identifiers to the latest annotations.
And then what? *or proteins, metabolites
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
tools
You get the latest pathway analysis tools...
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
February 2012 | Volume 8 | Issue 2
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
tools
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
February 2012 | Volume 8 | Issue 2
Huang et al., 2009
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
tools
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
February 2012 | Volume 8 | Issue 2
Khatri et al., 2012
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
tools
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
First generation - over representation analysis (ORA)
aka singular enrichment analysis (SEA)e.g. EASE, DAVID, IPA*
0. Use parametric statistics to identify DEGs, e.g. limma
1. Choose significance level e.g. FDR < 0.05, FC > 1.5
2. Use parametric statistics to identify annotations over represented within your list compared to what was assayed e.g. Fisher’s exact test
*disclosure – our department has a licensing agreement with Ingenuity Systems, Inc.
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
tools
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
First generation - over representation analysis (ORA)
Caveats:1. thresholdness – what about the transcript with p
= 0.050001, FC = 1.49992. equality, transcript-X with p = 0.0000001, FC =
100 considered equal to trans-Y p = 0.049, FC = 1.51
3. assumption of independence between both genes and pathways inflates significance
4. ignores relationships between genes/gene
products
5. significance increases with population size
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
tools
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
Second generation – gene set enrichment analysis (GSEA),
aka functional class scoring (FCS)e.g. GSEA, GlobalTest, Gazer, IPA
1. Use parametric statistics to determine DE for all genese.g. t-distribution statistics
2. Use various statistics to combine gene statistics and determine pathway statistics e.g. Wilcoxon rank sum, Kolmogorov-Smirnov
3. Permute phenotypes and pathways to determine pathway significance
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
tools
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
Second generation – gene set enrichment analysis (GSEA)
Overcomes most ORA limitations, except…
Caveats:
1. assumes independence between pathways
2. dependence on ranking approaches miss
magnitude of changes between phenotypes, i.e.,
sham FC = 10; treated similar FC = 100
3. ignores relationships between genes/gene
products
4. difficult/can not use your own special list - not an
issue for ORA
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
tools
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
Third generation – pathway topology (PT),aka modular enrichment analysis (MEA)
e.g. DAVID, SPIA, IPA
1. Use various statistics to determine differences in gene-gene* interactions** for all genese.g. Pearson’s correlation
2. Use various statistics to combine gene interaction statistics and determine pathway significance e.g. permutation, hypergeometric distribution
*aka node-node **edges
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
tools
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
Third generation – pathway topology (PT)
Caveats:1.limited interaction knowledge, i.e., thus hampered by immature interaction databases (KEGG, BioCarta, Reactome, PantherDB etc.)
Not to mention a lack of cellular and temporal resolution of interactions.
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
underlying statistics
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
Fisher’s exact test demonstration (if time permits)
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID
Keep in mind, before uploading:
1. does you list of DEGs contain gene’s expected a priori?
2. have you generated at least three* list’s with different cutoffs e.g. p < 0.05 / 0.01 , FC > 1.3 / 1.5
And after uploading:
are the pathway(s) expected a priori, identified in your analysis? *only for ORA analysis
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID
Withstood the test of time (released 2003)
1. proven functionality – highly cited
2. comprehensive – many databases accessible
3. feature rich – ORA, MEA, annotation
mapping, etc.
4. constantly updated & maintained – v6.7
5. well supported – personal experience
6. easy to use, well documented
7. free as in gratis
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID home
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID upload
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID list management
*Ariel Pink's Haunted Graffiti
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID background selection
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID functional annotation chart
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID functional annotation chart (options)
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID dowload results
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID results in spreadsheet
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID results in spreadsheet
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID functional annotation clustering
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
in use
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID functional annotation clustering
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
to summarise
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1. choose your analysis approach:
ORA if you must use your own special gene list
GSEA or PT, in addition to ORA, where possible
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
to summarise
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
DAVID
Khatri et al., 2012
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
to summarise
Probe Set ID
1434877_at
1419681_a_at
1451680_at
1436387_at
1437247_at
1416846_a_at
1439332_at
1419717_at
1436094_at
1452107_s_at
1442226_at
1433885_at
1419942_at
1418322_at
1427673_a_at
1426875_s_at
1454660_at
1429692_s_at
1436759_x_at
1456440_s_at
1429841_at
1439697_at
1436484_at
1444717_at
1456642_x_at
1455570_x_at
1425254_at
1456292_a_at
1456945_at
1428083_at
1438118_x_at
1433883_at
1443821_at
1449164_at
1450850_at
1448471_a_at
1451620_at
1456147_at
1451163_at
1425175_at
1418778_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1447972_at
1436010_at
1428564_at
1454824_s_at
1455516_at
1434203_at
1439548_at
1452405_x_at
1434742_s_at
1438377_x_at
1459886_at
1438910_a_at
1455447_at
1424396_a_at
1429719_at
1434930_at
1457157_at
1423777_at
1425506_at
1436204_at
1434277_a_at
1455765_a_at
1436736_x_at
1428910_at
1455158_at
1455870_at
1433992_at
1440975_at
1431088_at
1449187_at
1457003_at
1438407_at
1450121_at
1454758_a_at
1438474_at
1459703_at
1445815_at
1456295_at
1433909_at
1426724_at
1449007_at
1419905_s_at
1416811_s_at
1417357_at
1417235_at
1428622_at
1424734_at
1417818_at
1455165_at
1452010_at
1416529_at
1434510_at
1436659_at
1416632_at
1425162_at
1433842_at
1452887_at
1416749_at
1449322_at
1456380_x_at
1451230_a_at
1444908_at
1434769_at
1438848_at
1415845_at
1438251_x_at
1424050_s_at
1440612_at
1442032_at
1418480_at
1452158_at
1438023_at
1456785_at
1435294_at
1435484_at
1422673_at
1434869_at
1423579_a_at
1427338_at
1455328_at
1454803_a_at
1428744_s_at
1. choose your analysis approach:
ORA if you must use your own special gene list
GSEA or PT, in addition to ORA, where possible
2. use a range of cut-offs for ORA analysis
3. verify gene lists and pathway analysis output
with a priori biology
4. choose free (gratis & libre) tools where possible,
in addition to proprietary apps
Bioinformatics, Erasmus MCBioinformatics, Erasmus MC
questions?
k.brand@erasmusmc.
nl
