Mining Process Function Links
The column headings (line 1) are:
- 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_prob | process | function | genesInBoth | genesWithFunc | genesWithProc | probProcessGivenFunction | probFunctionGivenProcess | |||||||||||||||||
process_function_prob | GO:0009767-photosynthetic | electron | transport | chain | GO:0005375-copper | ion | transmembrane | transporter | activity | 1 | 76 | 128 | 0.0132 | 0.0078 | ||||||||||
process_function_prob | GO:0009767-photosynthetic | electron | transport | chain | GO:0005507-copper | ion | binding | 1 | 293 | 128 | 0.0034 | 0.0078 | ||||||||||||
process_function_prob | 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 | |||||
process_function_prob | GO:0009772-photosynthetic | electron | transport | in | photosystem | II | GO:0003959-NADPH | dehydrogenase | activity | 1 | 22 | 4 | 0.0455 | 0.2500 | ||||||||||
process_function_prob | 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 |
process_function_prob | GO:0009772-photosynthetic | electron | transport | in | photosystem | II | GO:0046428-1,4-dihydroxy-2-naphthoate | octaprenyltransferase | activity | 1 | 2 | 4 | 0.5000 | 0.2500 | ||||||||||
process_function_prob | GO:0009773-photosynthetic | electron | transport | in | photosystem | I | GO:0003677-DNA | binding | 1 | 9893 | 7 | 0.0001 | 0.1429 | |||||||||||
process_function_prob | GO:0009773-photosynthetic | electron | transport | in | photosystem | I | GO:0005516-calmodulin | binding | 1 | 373 | 7 | 0.0027 | 0.1429 | |||||||||||
process_function_prob | GO:0009773-photosynthetic | electron | transport | in | photosystem | I | GO:0009055-electron | carrier | activity | 1 | 1152 | 7 | 0.0009 | 0.1429 | ||||||||||
process_function_prob | 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 | |
process_function_prob | 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 | |
process_function_prob | GO:0010205-photoinhibition | GO:0004176-ATP-dependent | peptidase | activity | 1 | 56 | 7 | 0.0179 | 0.1429 | |||||||||||||||
process_function_prob | GO:0010205-photoinhibition | GO:0004722-protein | serine/threonine | phosphatase | activity | 1 | 417 | 7 | 0.0024 | 0.1429 | ||||||||||||||
process_function_prob | GO:0010205-photoinhibition | GO:0005198-structural | molecule | activity | 1 | 4123 | 7 | 0.0002 | 0.1429 | |||||||||||||||
process_function_prob | GO:0010205-photoinhibition | GO:0008237-metallopeptidase | activity | 1 | 481 | 7 | 0.0021 | 0.1429 | ||||||||||||||||
process_function_prob | GO:0010205-photoinhibition | GO:0008266-poly(U) | binding | 2 | 33 | 7 | 0.0606 | 0.2857 | ||||||||||||||||
process_function_prob | GO:0010205-photoinhibition | GO:0008270-zinc | ion | binding | 1 | 1396 | 7 | 0.0007 | 0.1429 | |||||||||||||||
process_function_prob | GO:0010205-photoinhibition | GO:0009979-16:0 | monogalactosyldiacylglycerol | desaturase | activity | 1 | 1 | 7 | 1.0000 | 0.1429 | ||||||||||||||
process_function_prob | GO:0010205-photoinhibition | GO:0010242-oxygen | evolving | activity | 2 | 2 | 7 | 1.0000 | 0.2857 | |||||||||||||||
process_function_prob | GO:0010205-photoinhibition | GO:0016887-ATPase | activity | 1 | 4197 | 7 | 0.0002 | 0.1429 | ||||||||||||||||
process_function_prob | GO:0010205-photoinhibition | GO:0045485-omega-6 | fatty | acid | desaturase | activity | 1 | 2 | 7 | 0.5000 | 0.1429 | |||||||||||||
process_function_prob | GO:0019684-photosynthesis, | light | reaction | GO:0008266-poly(U) | binding | 3 | 33 | 262 | 0.0909 | 0.0115 | ||||||||||||||
process_function_prob | GO:0019684-photosynthesis, | light | reaction | GO:0008839-dihydrodipicolinate | reductase | activity | 1 | 22 | 262 | 0.0455 | 0.0038 | |||||||||||||
process_function_prob | GO:0019684-photosynthesis, | light | reaction | GO:0010242-oxygen | evolving | activity | 2 | 2 | 262 | 1.0000 | 0.0076 | |||||||||||||
process_function_prob | GO:0019684-photosynthesis, | light | reaction | GO:0016168-chlorophyll | binding | 11 | 33 | 262 | 0.3333 | 0.0420 | ||||||||||||||
process_function_prob | GO:0019684-photosynthesis, | light | reaction | GO:0020037-heme | binding | 2 | 208 | 262 | 0.0096 | 0.0076 | ||||||||||||||
process_function_prob | GO:0019684-photosynthesis, | light | reaction | GO:0030385-ferredoxin:thioredoxin | reductase | activity | 2 | 4 | 262 | 0.5000 | 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.