Mining Process Function Links: Difference between revisions

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(New page: The column headings (line 1) are: #process_function_prob process function genesInBoth genesWithFunc genesWithProc probProcessGivenFunction probFunctionGivenProcess...)
 
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The column headings (line 1) are:
The column headings (line 1) are:


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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"
| #process_function_prob
|+ Process Function Links
|-
| process
| process
| function
| function
Line 30: Line 30:
| probFunctionGivenProcess
| probFunctionGivenProcess
|-
|-
| process_function_prob
| GO:0009767-photosynthetic
| GO:0009767-photosynthetic
| electron
| electron
Line 46: Line 45:
| 0.0078
| 0.0078
|-
|-
| process_function_prob
| GO:0009767-photosynthetic
| GO:0009767-photosynthetic
| electron
| electron
Line 60: Line 58:
| 0.0078
| 0.0078
|-
|-
| process_function_prob
| GO:0009767-photosynthetic
| GO:0009767-photosynthetic
| electron
| electron
Line 81: Line 78:
| 0.0078
| 0.0078
|-
|-
| process_function_prob
| GO:0009772-photosynthetic
| GO:0009772-photosynthetic
| electron
| electron
Line 97: Line 93:
| 0.2500
| 0.2500
|-
|-
| process_function_prob
| GO:0009772-photosynthetic
| GO:0009772-photosynthetic
| electron
| electron
Line 123: Line 118:
| 0.2500
| 0.2500
|-
|-
| process_function_prob
| GO:0009772-photosynthetic
| GO:0009772-photosynthetic
| electron
| electron
Line 139: Line 133:
| 0.2500
| 0.2500
|-
|-
| process_function_prob
| GO:0009773-photosynthetic
| GO:0009773-photosynthetic
| electron
| electron
Line 154: Line 147:
| 0.1429
| 0.1429
|-
|-
| process_function_prob
| GO:0009773-photosynthetic
| GO:0009773-photosynthetic
| electron
| electron
Line 169: Line 161:
| 0.1429
| 0.1429
|-
|-
| process_function_prob
| GO:0009773-photosynthetic
| GO:0009773-photosynthetic
| electron
| electron
Line 185: Line 176:
| 0.1429
| 0.1429
|-
|-
| process_function_prob
| GO:0009775-photosynthetic
| GO:0009775-photosynthetic
| electron
| electron
Line 210: Line 200:
| 0.4000
| 0.4000
|-
|-
| process_function_prob
| GO:0009775-photosynthetic
| GO:0009775-photosynthetic
| electron
| electron
Line 235: Line 224:
| 0.2000
| 0.2000
|-
|-
| process_function_prob
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0004176-ATP-dependent
| GO:0004176-ATP-dependent
Line 246: Line 234:
| 0.1429
| 0.1429
|-
|-
| process_function_prob
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0004722-protein
| GO:0004722-protein
Line 258: Line 245:
| 0.1429
| 0.1429
|-
|-
| process_function_prob
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0005198-structural
| GO:0005198-structural
Line 269: Line 255:
| 0.1429
| 0.1429
|-
|-
| process_function_prob
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0008237-metallopeptidase
| GO:0008237-metallopeptidase
Line 279: Line 264:
| 0.1429
| 0.1429
|-
|-
| process_function_prob
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0008266-poly(U)
| GO:0008266-poly(U)
Line 289: Line 273:
| 0.2857
| 0.2857
|-
|-
| process_function_prob
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0008270-zinc
| GO:0008270-zinc
Line 300: Line 283:
| 0.1429
| 0.1429
|-
|-
| process_function_prob
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0009979-16:0
| GO:0009979-16:0
Line 312: Line 294:
| 0.1429
| 0.1429
|-
|-
| process_function_prob
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0010242-oxygen
| GO:0010242-oxygen
Line 323: Line 304:
| 0.2857
| 0.2857
|-
|-
| process_function_prob
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0016887-ATPase
| GO:0016887-ATPase
Line 333: Line 313:
| 0.1429
| 0.1429
|-
|-
| process_function_prob
| GO:0010205-photoinhibition
| GO:0010205-photoinhibition
| GO:0045485-omega-6
| GO:0045485-omega-6
Line 346: Line 325:
| 0.1429
| 0.1429
|-
|-
| process_function_prob
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis,
| light
| light
Line 358: Line 336:
| 0.0115
| 0.0115
|-
|-
| process_function_prob
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis,
| light
| light
Line 371: Line 348:
| 0.0038
| 0.0038
|-
|-
| process_function_prob
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis,
| light
| light
Line 384: Line 360:
| 0.0076
| 0.0076
|-
|-
| process_function_prob
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis,
| light
| light
Line 396: Line 371:
| 0.0420
| 0.0420
|-
|-
| process_function_prob
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis,
| light
| light
Line 408: Line 382:
| 0.0076
| 0.0076
|-
|-
| process_function_prob
| GO:0019684-photosynthesis,
| GO:0019684-photosynthesis,
| light
| light
Line 421: Line 394:
| 0.0076
| 0.0076
|}
|}
Looking at the results, it appears to show that existing annotations do not support links in either direction. I would speculate that this is due to under-annotation.

Revision as of 16:38, 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 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, 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