Mining Process Function Links: Difference between revisions

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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
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


{|class="wikitable" style="text-align:center"
{|class="wikitable" style="text-align:center" border="1"
|+ Process Function Links
|-
|-
| process
| process
Line 30: Line 29:
| probFunctionGivenProcess
| probFunctionGivenProcess
|-
|-
| GO:0009767-photosynthetic
| GO:0009767-photosynthetic electron transport chain
| electron
| GO:0005375-copper ion transmembrane transporter activity
| transport
| chain
| GO:0005375-copper
| ion
| transmembrane
| transporter
| activity
| 1
| 1
| 76
| 76
Line 45: Line 37:
| 0.0078
| 0.0078
|-
|-
| GO:0009767-photosynthetic
| GO:0009767-photosynthetic electron transport chain
| electron
| GO:0005507-copper ion binding
| transport
| chain
| GO:0005507-copper
| ion
| binding
| 1
| 1
| 293
| 293
Line 58: Line 45:
| 0.0078
| 0.0078
|-
|-
| GO:0009767-photosynthetic
| GO:0009767-photosynthetic electron transport chain
| electron
| GO:0015662-ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism
| transport
| chain
| GO:0015662-ATPase
| activity,
| coupled
| to
| transmembrane
| movement
| of
| ions,
| phosphorylative
| mechanism
| 1
| 1
| 350
| 350
Line 78: Line 53:
| 0.0078
| 0.0078
|-
|-
| GO:0009772-photosynthetic
| GO:0009772-photosynthetic electron transport in photosystem II
| electron
| GO:0003959-NADPH dehydrogenase activity
| transport
| in
| photosystem
| II
| GO:0003959-NADPH
| dehydrogenase
| activity
| 1
| 1
| 22
| 22
Line 93: Line 61:
| 0.2500
| 0.2500
|-
|-
| GO:0009772-photosynthetic
| GO:0009772-photosynthetic electron transport in photosystem II
| electron
| GO:0045157-electron transporter, transferring electrons within the noncyclic electron transport pathway of photosynthesis activity
| transport
| in
| photosystem
| II
| GO:0045157-electron
| transporter,
| transferring
| electrons
| within
| the
| noncyclic
| electron
| transport
| pathway
| of
| photosynthesis
| activity
| 1
| 1
| 2
| 2
Line 118: Line 69:
| 0.2500
| 0.2500
|-
|-
| GO:0009772-photosynthetic
| GO:0009772-photosynthetic electron transport in photosystem II
| electron
| GO:0046428-1,4-dihydroxy-2-naphthoate octaprenyltransferase activity
| transport
| in
| photosystem
| II
| GO:0046428-1,4-dihydroxy-2-naphthoate
| octaprenyltransferase
| activity
| 1
| 1
| 2
| 2
Line 133: Line 77:
| 0.2500
| 0.2500
|-
|-
| GO:0009773-photosynthetic
| GO:0009773-photosynthetic electron transport in photosystem I
| electron
| GO:0003677-DNA binding
| transport
| in
| photosystem
| I
| GO:0003677-DNA
| binding
| 1
| 1
| 9893
| 9893
Line 147: Line 85:
| 0.1429
| 0.1429
|-
|-
| GO:0009773-photosynthetic
| GO:0009773-photosynthetic electron transport in photosystem I
| electron
| GO:0005516-calmodulin binding
| transport
| in
| photosystem
| I
| GO:0005516-calmodulin
| binding
| 1
| 1
| 373
| 373
Line 161: Line 93:
| 0.1429
| 0.1429
|-
|-
| GO:0009773-photosynthetic
| GO:0009773-photosynthetic electron transport in photosystem I
| electron
| GO:0009055-electron carrier activity
| transport
| in
| photosystem
| I
| GO:0009055-electron
| carrier
| activity
| 1
| 1
| 1152
| 1152
Line 176: Line 101:
| 0.1429
| 0.1429
|-
|-
| GO:0009775-photosynthetic
| GO:0009775-photosynthetic electron transport in cytochrome b6/f
| electron
| GO:0045158-electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
| transport
| in
| cytochrome
| b6/f
| GO:0045158-electron
| transporter,
| transferring
| electrons
| within
| cytochrome
| b6/f
| complex
| of
| photosystem
| II
| activity
| 2
| 2
| 2
| 2
Line 200: Line 109:
| 0.4000
| 0.4000
|-
|-
| GO:0009775-photosynthetic
| GO:0009775-photosynthetic electron transport in cytochrome b6/f
| electron
| GO:0046028-electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity
| transport
| in
| cytochrome
| b6/f
| GO:0046028-electron
| transporter,
| transferring
| electrons
| from
| cytochrome
| b6/f
| complex
| of
| photosystem
| II
| activity
| 1
| 1
| 1
| 1
Line 225: Line 118:
|-
|-
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0004176-ATP-dependent
| GO:0004176-ATP-dependent peptidase activity
| peptidase
| activity
| 1
| 1
| 56
| 56
Line 235: Line 126:
|-
|-
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0004722-protein
| GO:0004722-protein serine/threonine phosphatase activity
| serine/threonine
| phosphatase
| activity
| 1
| 1
| 417
| 417
Line 246: Line 134:
|-
|-
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0005198-structural
| GO:0005198-structural molecule activity
| molecule
| activity
| 1
| 1
| 4123
| 4123
Line 256: Line 142:
|-
|-
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0008237-metallopeptidase
| GO:0008237-metallopeptidase activity
| activity
| 1
| 1
| 481
| 481
Line 265: Line 150:
|-
|-
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0008266-poly(U)
| GO:0008266-poly(U) binding
| binding
| 2
| 2
| 33
| 33
Line 274: Line 158:
|-
|-
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0008270-zinc
| GO:0008270-zinc ion binding
| ion
| binding
| 1
| 1
| 1396
| 1396
Line 284: Line 166:
|-
|-
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0009979-16:0
| GO:0009979-16:0 monogalactosyldiacylglycerol desaturase activity
| monogalactosyldiacylglycerol
| desaturase
| activity
| 1
| 1
| 1
| 1
Line 295: Line 174:
|-
|-
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0010242-oxygen
| GO:0010242-oxygen evolving activity
| evolving
| activity
| 2
| 2
| 2
| 2
Line 305: Line 182:
|-
|-
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0016887-ATPase
| GO:0016887-ATPase activity
| activity
| 1
| 1
| 4197
| 4197
Line 314: Line 190:
|-
|-
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0045485-omega-6
| GO:0045485-omega-6 fatty acid desaturase activity
| fatty
| acid
| desaturase
| activity
| 1
| 1
| 2
| 2
Line 325: Line 197:
| 0.1429
| 0.1429
|-
|-
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis, light reaction
| light
| GO:0008266-poly(U) binding
| reaction
| GO:0008266-poly(U)
| binding
| 3
| 3
| 33
| 33
Line 336: Line 205:
| 0.0115
| 0.0115
|-
|-
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis, light reaction
| light
| GO:0008839-dihydrodipicolinate reductase activity
| reaction
| GO:0008839-dihydrodipicolinate
| reductase
| activity
| 1
| 1
| 22
| 22
Line 348: Line 213:
| 0.0038
| 0.0038
|-
|-
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis, light reaction
| light
| GO:0010242-oxygen evolving activity
| reaction
| GO:0010242-oxygen
| evolving
| activity
| 2
| 2
| 2
| 2
Line 360: Line 221:
| 0.0076
| 0.0076
|-
|-
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis, light reaction
| light
| GO:0016168-chlorophyll binding
| reaction
| GO:0016168-chlorophyll
| binding
| 11
| 11
| 33
| 33
Line 371: Line 229:
| 0.0420
| 0.0420
|-
|-
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis, light reaction
| light
| GO:0020037-heme binding
| reaction
| GO:0020037-heme
| binding
| 2
| 2
| 208
| 208
Line 382: Line 237:
| 0.0076
| 0.0076
|-
|-
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis, light reaction
| light
| GO:0030385-ferredoxin:thioredoxin reductase activity
| reaction
| GO:0030385-ferredoxin:thioredoxin
| reductase
| activity
| 2
| 2
| 4
| 4

Revision as of 16:40, 18 September 2008

The column headings (line 1) are:

  1. process_function_prob process function genesInBoth genesWithFunc genesWithProc probProcessGivenFunction probFunctionGivenProcess

The list shows various P and F pairs, and for each pair calculates statistics:

genesWithFunc = total genes annotated to F genesWithProc = total genes annotated to P

(IEAs excluded)

genesInBoth = total genes annotated to BOTH P and F.

probProcessGivenFunction = p(P | F) probFunctionGivenProcess = p(F | P)

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

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

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, transferring 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 activity 1 2 4 0.5000 0.2500
GO:0009773-photosynthetic electron transport in photosystem I GO:0003677-DNA binding 1 9893 7 0.0001 0.1429
GO:0009773-photosynthetic electron transport in photosystem I GO:0005516-calmodulin binding 1 373 7 0.0027 0.1429
GO:0009773-photosynthetic electron transport in photosystem I GO:0009055-electron carrier activity 1 1152 7 0.0009 0.1429
GO:0009775-photosynthetic electron transport in cytochrome b6/f GO:0045158-electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity 2 2 5 1.0000 0.4000
GO:0009775-photosynthetic electron transport in cytochrome b6/f GO:0046028-electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity 1 1 5 1.0000 0.2000
GO:0010205-photoinhibition GO:0004176-ATP-dependent peptidase activity 1 56 7 0.0179 0.1429
GO:0010205-photoinhibition GO:0004722-protein serine/threonine phosphatase activity 1 417 7 0.0024 0.1429
GO:0010205-photoinhibition GO:0005198-structural molecule activity 1 4123 7 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
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