title: "All T2D vs NGT Related Results"
  author: "Andy Beck"
  date: "Thursday, May 14, 2015"

In this report we are only concerned with T2D versus NGT ("case versus control"). Differential expression results were corrected for multiple testing using Story's Q (using bioconductor package qvalue).

For the first two sections of this report, the cut-off for differential expression is FDR \(\leq\) 0.1. For the later sections of the report we mark the (300/500/1000/2000) most significant pvalues as being differentially expressed. We display at minimum 5 categories for each trait, and at most 20, ordered by significance.

Gene length for bias correction; Wallenius approximation

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Number of significant GO categories: 3

Number of DE genes: 320

category term numInCat numDEInCat q.value
GO:0022904 respiratory electron transport chain 105 11 0.0048269
GO:0022900 electron transport chain 106 11 0.0048269
GO:0045333 cellular respiration 158 13 0.0075522
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 6 0.1179422
GO:0042773 ATP synthesis coupled electron transport 54 6 0.3650270

Using median counts for bias correction; Wallenius Approximation

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Number of significant GO categories: 0

Number of DE genes: 320

category term numInCat numDEInCat q.value
GO:0022904 respiratory electron transport chain 105 11 1
GO:0022900 electron transport chain 106 11 1
GO:0045333 cellular respiration 158 13 1
GO:0050882 voluntary musculoskeletal movement 3 2 1
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 6 1

For the next set of results, we look at the impact of number of differentially expressed genes (300, 500, 1000, and 2000).

300 genes DE; length bias corrected; Wallenius approximation

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Number of significant GO categories: 3

Number of DE genes: 300

category term numInCat numDEInCat q.value
GO:0022904 respiratory electron transport chain 105 11 0.0027595
GO:0022900 electron transport chain 106 11 0.0027595
GO:0045333 cellular respiration 158 12 0.0237158
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 6 0.0862372
GO:0042773 ATP synthesis coupled electron transport 54 6 0.2685357

300 genes DE; count bias corrected; Wallenius approximation

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Number of significant GO categories: 0

Number of DE genes: 300

category term numInCat numDEInCat q.value
GO:0022904 respiratory electron transport chain 105 11 1
GO:0022900 electron transport chain 106 11 1
GO:0050882 voluntary musculoskeletal movement 3 2 1
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 6 1
GO:0045333 cellular respiration 158 12 1

500 genes DE; length bias corrected; Wallenius approximation

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Number of significant GO categories: 2

Number of DE genes: 500

category term numInCat numDEInCat q.value
GO:0022904 respiratory electron transport chain 105 13 0.0124470
GO:0022900 electron transport chain 106 13 0.0124470
GO:0045333 cellular respiration 158 15 0.0575483
GO:2001256 regulation of store-operated calcium entry 5 3 0.8274762
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 6 1.0000000

500 genes DE; count bias corrected; Wallenius approximation

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Number of significant GO categories: 0

Number of DE genes: 500

category term numInCat numDEInCat q.value
GO:2001256 regulation of store-operated calcium entry 5 3 1
GO:0055091 phospholipid homeostasis 7 3 1
GO:0002115 store-operated calcium entry 8 3 1
GO:0022904 respiratory electron transport chain 105 13 1
GO:0022900 electron transport chain 106 13 1

1000 genes DE; length bias corrected; Wallenius approximation

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Number of significant GO categories: 16

Number of DE genes: 1000

category term numInCat numDEInCat q.value
GO:0022904 respiratory electron transport chain 105 32 0.0000000
GO:0022900 electron transport chain 106 32 0.0000000
GO:0045333 cellular respiration 158 35 0.0000000
GO:1902600 hydrogen ion transmembrane transport 84 21 0.0000020
GO:0055114 oxidation-reduction process 895 90 0.0000148
GO:0006091 generation of precursor metabolites and energy 395 50 0.0000281
GO:0015980 energy derivation by oxidation of organic compounds 319 43 0.0000325
GO:0042773 ATP synthesis coupled electron transport 54 15 0.0000325
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 15 0.0000325
GO:0015992 proton transport 112 21 0.0002193
GO:0006818 hydrogen transport 114 21 0.0002873
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 12 0.0003775
GO:0006119 oxidative phosphorylation 70 15 0.0011039
GO:0015985 energy coupled proton transport, down electrochemical gradient 19 7 0.0124564
GO:0015986 ATP synthesis coupled proton transport 19 7 0.0124564
GO:0042776 mitochondrial ATP synthesis coupled proton transport 14 6 0.0184776

1000 genes DE; count bias corrected; Wallenius approximation

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Number of significant GO categories: 5

Number of DE genes: 1000

category term numInCat numDEInCat q.value
GO:0022904 respiratory electron transport chain 105 32 0.0000033
GO:0022900 electron transport chain 106 32 0.0000033
GO:0045333 cellular respiration 158 35 0.0007728
GO:1902600 hydrogen ion transmembrane transport 84 21 0.0030263
GO:0055114 oxidation-reduction process 895 90 0.0483752

2000 genes DE; count bias corrected; Wallenius approximation

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Number of significant GO categories: 23

Number of DE genes: 2000

category term numInCat numDEInCat q.value
GO:0022904 respiratory electron transport chain 105 47 0.0000000
GO:0022900 electron transport chain 106 47 0.0000000
GO:0045333 cellular respiration 158 55 0.0000000
GO:1902600 hydrogen ion transmembrane transport 84 32 0.0000000
GO:0015980 energy derivation by oxidation of organic compounds 319 75 0.0000000
GO:0006091 generation of precursor metabolites and energy 395 86 0.0000000
GO:0055114 oxidation-reduction process 895 154 0.0000002
GO:0015992 proton transport 112 34 0.0000024
GO:0006818 hydrogen transport 114 34 0.0000038
GO:0042773 ATP synthesis coupled electron transport 54 21 0.0000099
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 21 0.0000099
GO:0015985 energy coupled proton transport, down electrochemical gradient 19 12 0.0000126
GO:0015986 ATP synthesis coupled proton transport 19 12 0.0000126
GO:0006119 oxidative phosphorylation 70 23 0.0000786
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 16 0.0005121
GO:0006754 ATP biosynthetic process 36 15 0.0006086
GO:0042776 mitochondrial ATP synthesis coupled proton transport 14 9 0.0006173
GO:0009127 purine nucleoside monophosphate biosynthetic process 61 19 0.0042433
GO:0009168 purine ribonucleoside monophosphate biosynthetic process 61 19 0.0042433
GO:0009145 purine nucleoside triphosphate biosynthetic process 47 16 0.0049082

2000 genes DE; count bias corrected; Wallenius approximation

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Number of significant GO categories: 14

Number of DE genes: 2000

category term numInCat numDEInCat q.value
GO:0022904 respiratory electron transport chain 105 47 0.0000000
GO:0022900 electron transport chain 106 47 0.0000000
GO:0045333 cellular respiration 158 55 0.0000014
GO:1902600 hydrogen ion transmembrane transport 84 32 0.0000500
GO:0055114 oxidation-reduction process 895 154 0.0011656
GO:0015992 proton transport 112 34 0.0018547
GO:0015980 energy derivation by oxidation of organic compounds 319 75 0.0018547
GO:0006818 hydrogen transport 114 34 0.0023206
GO:0015985 energy coupled proton transport, down electrochemical gradient 19 12 0.0044917
GO:0015986 ATP synthesis coupled proton transport 19 12 0.0044917
GO:0006091 generation of precursor metabolites and energy 395 86 0.0045197
GO:0042773 ATP synthesis coupled electron transport 54 21 0.0175063
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 21 0.0175063
GO:0006754 ATP biosynthetic process 36 15 0.0406657