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| The column headings (line 1) are:
| | == Using existing annotations == |
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| #process_function_prob process function genesInBoth genesWithFunc genesWithProc probProcessGivenFunction probFunctionGivenProcess
| | [[Mining_Process_Function_Links_from_Annotations]] |
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| The list shows various P and F pairs, and for each pair calculates statistics:
| | Drawbacks: |
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| |
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| genesWithFunc = total genes annotated to F
| | * incomplete annotations |
| genesWithProc = total genes annotated to P
| | * annotation bias |
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|
| (IEAs excluded)
| | == Using Pathway Databases == |
|
| |
|
| genesInBoth = total genes annotated to BOTH P and F.
| | [[Mining_Process_Function_Links_from_Reactome]] |
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| probProcessGivenFunction = p(P | F)
| | == Using Obol == |
| probFunctionGivenProcess = p(F | P)
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|
| |
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| if p(P | F) is high and we have a statistically significant sample size, then there is support for a F part_of P link
| | [[XP:biological_process_xp_molecular_function]] |
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| if p(F | P) is high and we have a statistically significant sample size, then there is support for a P has_part F link
| | [[Category:Ontology]] |
| | | [[Category:Function-Process]] |
| {|class="wikitable" style="text-align:center"
| | [[Category:Electron transport]] |
| |+ Process Function Links
| |
| |-
| |
| | process
| |
| | function
| |
| | genesInBoth
| |
| | genesWithFunc
| |
| | genesWithProc
| |
| | probProcessGivenFunction
| |
| | probFunctionGivenProcess
| |
| |-
| |
| | GO:0009767-photosynthetic
| |
| | electron
| |
| | transport
| |
| | chain
| |
| | GO:0005375-copper
| |
| | ion
| |
| | transmembrane
| |
| | transporter
| |
| | activity
| |
| | 1
| |
| | 76
| |
| | 128
| |
| | 0.0132
| |
| | 0.0078
| |
| |-
| |
| | GO:0009767-photosynthetic
| |
| | electron
| |
| | transport
| |
| | chain
| |
| | GO:0005507-copper
| |
| | ion
| |
| | binding
| |
| | 1
| |
| | 293
| |
| | 128
| |
| | 0.0034
| |
| | 0.0078
| |
| |-
| |
| | GO:0009767-photosynthetic
| |
| | electron
| |
| | transport
| |
| | chain
| |
| | GO:0015662-ATPase
| |
| | activity,
| |
| | coupled
| |
| | to
| |
| | transmembrane
| |
| | movement
| |
| | of
| |
| | ions,
| |
| | phosphorylative
| |
| | mechanism
| |
| | 1
| |
| | 350
| |
| | 128
| |
| | 0.0029
| |
| | 0.0078
| |
| |-
| |
| | GO:0009772-photosynthetic
| |
| | electron
| |
| | transport
| |
| | in
| |
| | photosystem
| |
| | II
| |
| | GO:0003959-NADPH
| |
| | dehydrogenase
| |
| | activity
| |
| | 1
| |
| | 22
| |
| | 4
| |
| | 0.0455
| |
| | 0.2500
| |
| |-
| |
| | GO:0009772-photosynthetic
| |
| | electron
| |
| | transport
| |
| | in
| |
| | photosystem
| |
| | II
| |
| | GO:0045157-electron
| |
| | transporter,
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| | transferring
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| | electrons
| |
| | within
| |
| | the
| |
| | noncyclic
| |
| | electron
| |
| | transport
| |
| | pathway
| |
| | of
| |
| | photosynthesis
| |
| | activity
| |
| | 1
| |
| | 2
| |
| | 4
| |
| | 0.5000
| |
| | 0.2500
| |
| |-
| |
| | GO:0009772-photosynthetic
| |
| | electron
| |
| | transport
| |
| | in
| |
| | photosystem
| |
| | II
| |
| | GO:0046428-1,4-dihydroxy-2-naphthoate
| |
| | octaprenyltransferase
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| | activity
| |
| | 1
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| | 2
| |
| | 4
| |
| | 0.5000
| |
| | 0.2500
| |
| |-
| |
| | GO:0009773-photosynthetic
| |
| | electron
| |
| | transport
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| | in
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| | photosystem
| |
| | I
| |
| | GO:0003677-DNA
| |
| | binding
| |
| | 1
| |
| | 9893
| |
| | 7
| |
| | 0.0001
| |
| | 0.1429
| |
| |-
| |
| | GO:0009773-photosynthetic
| |
| | electron
| |
| | transport
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| | in
| |
| | photosystem
| |
| | I
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| | GO:0005516-calmodulin
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| | binding
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| | 1
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| | 373
| |
| | 7
| |
| | 0.0027
| |
| | 0.1429
| |
| |-
| |
| | GO:0009773-photosynthetic
| |
| | electron
| |
| | transport
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| | in
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| | photosystem
| |
| | I
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| | GO:0009055-electron
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| | carrier
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| | activity
| |
| | 1
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| | 1152
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| | 7
| |
| | 0.0009
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| | 0.1429
| |
| |-
| |
| | GO:0009775-photosynthetic
| |
| | electron
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| | transport
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| | in
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| | cytochrome
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| | b6/f
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| | GO:0045158-electron
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| | transporter,
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| | transferring
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| | electrons
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| | within
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| | cytochrome
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| | b6/f
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| | complex
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| | of
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| | photosystem
| |
| | II
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| | activity
| |
| | 2
| |
| | 2
| |
| | 5
| |
| | 1.0000
| |
| | 0.4000
| |
| |-
| |
| | GO:0009775-photosynthetic
| |
| | electron
| |
| | transport
| |
| | in
| |
| | cytochrome
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| | b6/f
| |
| | GO:0046028-electron
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| | transporter,
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| | transferring
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| | electrons
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| | from
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| | cytochrome
| |
| | b6/f
| |
| | complex
| |
| | of
| |
| | photosystem
| |
| | II
| |
| | activity
| |
| | 1
| |
| | 1
| |
| | 5
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| | 1.0000
| |
| | 0.2000
| |
| |-
| |
| | GO:0010205-photoinhibition
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| | GO:0004176-ATP-dependent
| |
| | peptidase
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| | activity
| |
| | 1
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| | 56
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| | 7
| |
| | 0.0179
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| | 0.1429
| |
| |-
| |
| | GO:0010205-photoinhibition
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| | GO:0004722-protein
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| | serine/threonine
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| | phosphatase
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| | activity
| |
| | 1
| |
| | 417
| |
| | 7
| |
| | 0.0024
| |
| | 0.1429
| |
| |-
| |
| | GO:0010205-photoinhibition
| |
| | GO:0005198-structural
| |
| | molecule
| |
| | activity
| |
| | 1
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| | 4123
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| | 7
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| | 0.0002
| |
| | 0.1429
| |
| |-
| |
| | GO:0010205-photoinhibition
| |
| | GO:0008237-metallopeptidase
| |
| | activity
| |
| | 1
| |
| | 481
| |
| | 7
| |
| | 0.0021
| |
| | 0.1429
| |
| |-
| |
| | GO:0010205-photoinhibition
| |
| | GO:0008266-poly(U)
| |
| | binding
| |
| | 2
| |
| | 33
| |
| | 7
| |
| | 0.0606
| |
| | 0.2857
| |
| |-
| |
| | GO:0010205-photoinhibition
| |
| | GO:0008270-zinc
| |
| | ion
| |
| | binding
| |
| | 1
| |
| | 1396
| |
| | 7
| |
| | 0.0007
| |
| | 0.1429
| |
| |-
| |
| | GO:0010205-photoinhibition
| |
| | GO:0009979-16:0
| |
| | monogalactosyldiacylglycerol
| |
| | desaturase
| |
| | activity
| |
| | 1
| |
| | 1
| |
| | 7
| |
| | 1.0000
| |
| | 0.1429
| |
| |-
| |
| | GO:0010205-photoinhibition
| |
| | GO:0010242-oxygen
| |
| | evolving
| |
| | activity
| |
| | 2
| |
| | 2
| |
| | 7
| |
| | 1.0000
| |
| | 0.2857
| |
| |-
| |
| | GO:0010205-photoinhibition
| |
| | GO:0016887-ATPase
| |
| | activity
| |
| | 1
| |
| | 4197
| |
| | 7
| |
| | 0.0002
| |
| | 0.1429
| |
| |-
| |
| | GO:0010205-photoinhibition
| |
| | GO:0045485-omega-6
| |
| | fatty
| |
| | acid
| |
| | desaturase
| |
| | activity
| |
| | 1
| |
| | 2
| |
| | 7
| |
| | 0.5000
| |
| | 0.1429
| |
| |-
| |
| | GO:0019684-photosynthesis,
| |
| | light
| |
| | reaction
| |
| | GO:0008266-poly(U)
| |
| | binding
| |
| | 3
| |
| | 33
| |
| | 262
| |
| | 0.0909
| |
| | 0.0115
| |
| |-
| |
| | GO:0019684-photosynthesis,
| |
| | light
| |
| | reaction
| |
| | GO:0008839-dihydrodipicolinate
| |
| | reductase
| |
| | activity
| |
| | 1
| |
| | 22
| |
| | 262
| |
| | 0.0455
| |
| | 0.0038
| |
| |-
| |
| | GO:0019684-photosynthesis,
| |
| | light
| |
| | reaction
| |
| | GO:0010242-oxygen
| |
| | evolving
| |
| | activity
| |
| | 2
| |
| | 2
| |
| | 262
| |
| | 1.0000
| |
| | 0.0076
| |
| |-
| |
| | GO:0019684-photosynthesis,
| |
| | light
| |
| | reaction
| |
| | GO:0016168-chlorophyll
| |
| | binding
| |
| | 11
| |
| | 33
| |
| | 262
| |
| | 0.3333
| |
| | 0.0420
| |
| |-
| |
| | GO:0019684-photosynthesis,
| |
| | light
| |
| | reaction
| |
| | GO:0020037-heme
| |
| | binding
| |
| | 2
| |
| | 208
| |
| | 262
| |
| | 0.0096
| |
| | 0.0076
| |
| |-
| |
| | GO:0019684-photosynthesis,
| |
| | light
| |
| | reaction
| |
| | GO:0030385-ferredoxin:thioredoxin
| |
| | reductase
| |
| | activity
| |
| | 2
| |
| | 4
| |
| | 262
| |
| | 0.5000
| |
| | 0.0076
| |
| |}
| |