This notebook demonstrates summarizing annotation counts for a term and its descendants.
An example use of this is a GO annotator exploring refactoring a subtree in GO
Of course, if this were a regular thing we would make a command line or even web interface, but keeping as a notebook gives us some flexibility in logic, and anyway is intended largely as a demonstration
import pandas as pd
## Create an ontology factory in order to fetch GO
from ontobio.ontol_factory import OntologyFactory
ofactory = OntologyFactory()
## GOLR queries
from ontobio.golr.golr_query import GolrAssociationQuery
## rendering ontologies
from ontobio import GraphRenderer
## Load GO. Note the first time this runs Jupyter will show '*' - be patient
ont = ofactory.create("go")
Here we are using the in-memory ontology object, no external service calls are executed
Change the value of term_id
to what you like
term_id = "GO:0009070" ## serine family amino acid biosynthetic process
descendants = ont.descendants(term_id, reflexive=True, relations=['subClassOf', 'BFO:0000050'])
descendants
['GO:0016260', 'GO:0004124', 'GO:0019343', 'GO:0019265', 'GO:0019345', 'GO:0006564', 'GO:0006545', 'GO:0071269', 'GO:0006535', 'GO:0009090', 'GO:0070179', 'GO:0019264', 'GO:0009070', 'GO:0019344']
We use the good-old-fashioned Tree renderer
(this doesn't scale well for latticey-subontologies)
renderer = GraphRenderer.create('tree')
print(renderer.render_subgraph(ont, nodes=descendants))
. GO:0009070 ! serine family amino acid biosynthetic process % GO:0006545 ! glycine biosynthetic process % GO:0019264 ! glycine biosynthetic process from serine % GO:0019265 ! glycine biosynthetic process, by transamination of glyoxylate % GO:0006564 ! L-serine biosynthetic process % GO:0019344 ! cysteine biosynthetic process % GO:0006535 ! cysteine biosynthetic process from serine % GO:0019343 ! cysteine biosynthetic process via cystathionine % GO:0019345 ! cysteine biosynthetic process via S-sulfo-L-cysteine < GO:0004124 ! cysteine synthase activity % GO:0009090 ! homoserine biosynthetic process % GO:0016260 ! selenocysteine biosynthetic process % GO:0070179 ! D-serine biosynthetic process % GO:0071269 ! L-homocysteine biosynthetic process
We write a short procedure to wrap calling Golr and returning a summary dict
The dict is keyed by taxon label. We also include an entry for ALL
DEFAULT_FACET_FIELDS = ['taxon_subset_closure_label', 'evidence_label', 'assigned_by']
def summarize(t: str,
evidence_closure='ECO:0000269', ## restrict to experimental
facet_fields=None) -> dict:
"""
Summarize a term
"""
if facet_fields == None:
facet_fields = DEFAULT_FACET_FIELDS
q = GolrAssociationQuery(object=t, rows=0, object_category='function',
fq={'evidence_closur'taxon_subset_closure_label'e_label':'experimental evidence'},
facet_fields=facet_fields)
#params = q.solr_params()
#print(params)
result = q.exec()
fc = result['facet_counts']
item = {'ALL': result['numFound']} ## make sure this is the first entry
for ff in facet_fields:
if ff in fc:
item.update(fc[ff])
return item
print(summarize(term_id))
{'ALL': 144, 'Eukaryota': 92, 'Bacteria': 52, 'Metazoa': 33, 'Fungi': 32, 'Escherichia coli K-12': 27, 'Viridiplantae': 23, 'Mammalia': 22, 'Vertebrata <vertebrates>': 22, 'Arabidopsis thaliana': 21, 'Saccharomyces cerevisiae S288C': 17, 'Mycobacterium tuberculosis H37Rv': 11, 'Schizosaccharomyces pombe': 11, 'Homo sapiens': 8, 'Caenorhabditis elegans': 7, 'Mus musculus': 7, 'Rattus norvegicus': 7, 'Bacillus subtilis subsp. subtilis str. 168': 6, 'Pseudomonas aeruginosa PAO1': 4, 'Aspergillus nidulans FGSC A4': 3, 'Apis mellifera': 2, 'Leishmania major strain Friedlin': 2, 'Bombyx mori': 1, 'Candida albicans SC5314': 1, 'Dictyostelium discoideum': 1, 'Drosophila melanogaster': 1, 'direct assay evidence used in manual assertion': 81, 'mutant phenotype evidence used in manual assertion': 53, 'genetic interaction evidence used in manual assertion': 10, 'EcoCyc': 20, 'TAIR': 19, 'SGD': 17, 'UniProt': 16, 'PomBase': 11, 'MTBBASE': 10, 'EcoliWiki': 7, 'RGD': 7, 'WB': 7, 'MGI': 6, 'CAFA': 5, 'PseudoCAP': 5, 'BHF-UCL': 4, 'AspGD': 3, 'GeneDB': 3, 'CGD': 1, 'FlyBase': 1, 'GOC': 1, 'dictyBase': 1}
def summarize_set(ids, facet_fields=None) -> pd.DataFrame:
"""
Summarize a set of annotations, return a dataframe
"""
items = []
for id in ids:
item = {'id': id, 'name:': ont.label(id)}
for k,v in summarize(id, facet_fields=facet_fields).items():
item[k] = v
items.append(item)
df = pd.DataFrame(items).fillna(0)
# sort using total number
df.sort_values('ALL', axis=0, ascending=False, inplace=True)
return df
More advanced visualziations are easy with plotly etc. We leave as an exercise to the reader...
As an example, for the first query we bundle all facets (species, evidence, assigned by) together
pd.options.display.max_columns = None
df = summarize_set(descendants)
df
id | name: | ALL | Bacteria | Escherichia coli K-12 | Eukaryota | Mammalia | Metazoa | Mus musculus | Trypanosoma brucei brucei TREU927 | Vertebrata <vertebrates> | mutant phenotype evidence used in manual assertion | direct assay evidence used in manual assertion | EcoCyc | GeneDB | MGI | Viridiplantae | Arabidopsis thaliana | Fungi | Caenorhabditis elegans | Schizosaccharomyces pombe | Bacillus subtilis subsp. subtilis str. 168 | Mycobacterium tuberculosis H37Rv | Saccharomyces cerevisiae S288C | Solanum tuberosum | Spinacia oleracea | Streptomyces lavendulae | genetic interaction evidence used in manual assertion | TAIR | PomBase | UniProt | WB | CAFA | EcoliWiki | MTBBASE | SGD | Aspergillus nidulans FGSC A4 | Apis mellifera | Homo sapiens | Leishmania major strain Friedlin | AspGD | BHF-UCL | Rattus norvegicus | RGD | Pseudomonas aeruginosa PAO1 | Thermus thermophilus HB27 | PseudoCAP | Bombyx mori | Drosophila melanogaster | FlyBase | Lactobacillus casei | Candida albicans SC5314 | CGD | Dictyostelium discoideum | dictyBase | GOC | Pseudomonas aeruginosa | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
12 | GO:0009070 | serine family amino acid biosynthetic process | 144 | 52.0 | 27.0 | 92.0 | 22.0 | 33.0 | 7.0 | 0.0 | 22.0 | 53.0 | 81.0 | 20.0 | 3.0 | 6.0 | 23.0 | 21.0 | 32.0 | 7.0 | 11.0 | 6.0 | 11.0 | 17.0 | 0.0 | 0.0 | 0.0 | 10.0 | 19.0 | 11.0 | 16.0 | 7.0 | 5.0 | 7.0 | 10.0 | 17.0 | 3.0 | 2.0 | 8.0 | 2.0 | 3.0 | 4.0 | 7.0 | 7.0 | 4.0 | 0.0 | 5.0 | 1.0 | 1.0 | 1.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 0.0 |
13 | GO:0019344 | cysteine biosynthetic process | 82 | 25.0 | 8.0 | 57.0 | 6.0 | 15.0 | 2.0 | 0.0 | 6.0 | 30.0 | 49.0 | 6.0 | 2.0 | 1.0 | 21.0 | 19.0 | 19.0 | 7.0 | 10.0 | 5.0 | 8.0 | 6.0 | 1.0 | 1.0 | 0.0 | 3.0 | 17.0 | 10.0 | 10.0 | 7.0 | 5.0 | 2.0 | 7.0 | 6.0 | 3.0 | 2.0 | 3.0 | 2.0 | 3.0 | 2.0 | 1.0 | 1.0 | 1.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 |
1 | GO:0004124 | cysteine synthase activity | 29 | 7.0 | 3.0 | 22.0 | 0.0 | 4.0 | 0.0 | 0.0 | 0.0 | 6.0 | 21.0 | 2.0 | 0.0 | 0.0 | 13.0 | 11.0 | 5.0 | 4.0 | 4.0 | 2.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 2.0 | 10.0 | 4.0 | 4.0 | 4.0 | 2.0 | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
5 | GO:0006564 | L-serine biosynthetic process | 21 | 16.0 | 8.0 | 5.0 | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 9.0 | 6.0 | 3.0 | 0.0 | 0.0 | 1.0 | 1.0 | 3.0 | 0.0 | 0.0 | 1.0 | 3.0 | 3.0 | 0.0 | 0.0 | 0.0 | 6.0 | 1.0 | 0.0 | 2.0 | 0.0 | 0.0 | 5.0 | 3.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 3.0 | 1.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
8 | GO:0006535 | cysteine biosynthetic process from serine | 20 | 9.0 | 4.0 | 11.0 | 0.0 | 4.0 | 0.0 | 0.0 | 0.0 | 6.0 | 13.0 | 3.0 | 1.0 | 0.0 | 0.0 | 0.0 | 6.0 | 3.0 | 5.0 | 2.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 5.0 | 2.0 | 3.0 | 2.0 | 1.0 | 2.0 | 1.0 | 0.0 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
6 | GO:0006545 | glycine biosynthetic process | 14 | 3.0 | 3.0 | 11.0 | 7.0 | 9.0 | 0.0 | 0.0 | 7.0 | 2.0 | 11.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 1.0 | 5.0 | 5.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
2 | GO:0019343 | cysteine biosynthetic process via cystathionine | 9 | 1.0 | 0.0 | 8.0 | 1.0 | 2.0 | 0.0 | 0.0 | 1.0 | 6.0 | 3.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 5.0 | 0.0 | 0.0 | 0.0 | 1.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | 3.0 | 2.0 | 1.0 | 1.0 | 1.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
9 | GO:0009090 | homoserine biosynthetic process | 8 | 4.0 | 4.0 | 4.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 4.0 | 4.0 | 4.0 | 0.0 | 0.0 | 0.0 | 0.0 | 4.0 | 0.0 | 0.0 | 0.0 | 0.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 |
10 | GO:0070179 | D-serine biosynthetic process | 8 | 0.0 | 0.0 | 8.0 | 6.0 | 6.0 | 4.0 | 0.0 | 6.0 | 0.0 | 8.0 | 0.0 | 0.0 | 4.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 |
0 | GO:0016260 | selenocysteine biosynthetic process | 6 | 4.0 | 4.0 | 2.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 4.0 | 2.0 | 4.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
11 | GO:0019264 | glycine biosynthetic process from serine | 6 | 2.0 | 2.0 | 4.0 | 2.0 | 4.0 | 0.0 | 0.0 | 2.0 | 2.0 | 4.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 2.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
3 | GO:0019265 | glycine biosynthetic process, by transaminatio... | 4 | 0.0 | 0.0 | 4.0 | 3.0 | 3.0 | 0.0 | 0.0 | 3.0 | 0.0 | 4.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
7 | GO:0071269 | L-homocysteine biosynthetic process | 1 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
4 | GO:0019345 | cysteine biosynthetic process via S-sulfo-L-cy... | 0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
summarize_set(descendants, facet_fields=['assigned_by'])
id | name: | ALL | EcoCyc | GeneDB | MGI | TAIR | PomBase | UniProt | WB | CAFA | EcoliWiki | MTBBASE | SGD | AspGD | BHF-UCL | RGD | PseudoCAP | FlyBase | CGD | dictyBase | GOC | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
12 | GO:0009070 | serine family amino acid biosynthetic process | 144 | 20.0 | 3.0 | 6.0 | 19.0 | 11.0 | 16.0 | 7.0 | 5.0 | 7.0 | 10.0 | 17.0 | 3.0 | 4.0 | 7.0 | 5.0 | 1.0 | 1.0 | 1.0 | 1.0 |
13 | GO:0019344 | cysteine biosynthetic process | 82 | 6.0 | 2.0 | 1.0 | 17.0 | 10.0 | 10.0 | 7.0 | 5.0 | 2.0 | 7.0 | 6.0 | 3.0 | 2.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 1.0 |
1 | GO:0004124 | cysteine synthase activity | 29 | 2.0 | 0.0 | 0.0 | 10.0 | 4.0 | 4.0 | 4.0 | 2.0 | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
5 | GO:0006564 | L-serine biosynthetic process | 21 | 3.0 | 0.0 | 0.0 | 1.0 | 0.0 | 2.0 | 0.0 | 0.0 | 5.0 | 3.0 | 3.0 | 0.0 | 0.0 | 1.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 |
8 | GO:0006535 | cysteine biosynthetic process from serine | 20 | 3.0 | 1.0 | 0.0 | 0.0 | 5.0 | 2.0 | 3.0 | 2.0 | 1.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
6 | GO:0006545 | glycine biosynthetic process | 14 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 1.0 | 5.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 |
2 | GO:0019343 | cysteine biosynthetic process via cystathionine | 9 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | 3.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
9 | GO:0009090 | homoserine biosynthetic process | 8 | 4.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 |
10 | GO:0070179 | D-serine biosynthetic process | 8 | 0.0 | 0.0 | 4.0 | 1.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
0 | GO:0016260 | selenocysteine biosynthetic process | 6 | 4.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
11 | GO:0019264 | glycine biosynthetic process from serine | 6 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 |
3 | GO:0019265 | glycine biosynthetic process, by transaminatio... | 4 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
7 | GO:0071269 | L-homocysteine biosynthetic process | 1 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
4 | GO:0019345 | cysteine biosynthetic process via S-sulfo-L-cy... | 0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
use taxon_subset_closure_label
facet
summarize_set(descendants, facet_fields=['taxon_subset_closure_label'])
id | name: | ALL | Bacteria | Escherichia coli K-12 | Eukaryota | Mammalia | Metazoa | Mus musculus | Trypanosoma brucei brucei TREU927 | Vertebrata <vertebrates> | Viridiplantae | Arabidopsis thaliana | Fungi | Caenorhabditis elegans | Schizosaccharomyces pombe | Bacillus subtilis subsp. subtilis str. 168 | Mycobacterium tuberculosis H37Rv | Saccharomyces cerevisiae S288C | Solanum tuberosum | Spinacia oleracea | Streptomyces lavendulae | Aspergillus nidulans FGSC A4 | Apis mellifera | Homo sapiens | Leishmania major strain Friedlin | Rattus norvegicus | Pseudomonas aeruginosa PAO1 | Thermus thermophilus HB27 | Bombyx mori | Drosophila melanogaster | Lactobacillus casei | Candida albicans SC5314 | Dictyostelium discoideum | Pseudomonas aeruginosa | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
12 | GO:0009070 | serine family amino acid biosynthetic process | 144 | 52.0 | 27.0 | 92.0 | 22.0 | 33.0 | 7.0 | 0.0 | 22.0 | 23.0 | 21.0 | 32.0 | 7.0 | 11.0 | 6.0 | 11.0 | 17.0 | 0.0 | 0.0 | 0.0 | 3.0 | 2.0 | 8.0 | 2.0 | 7.0 | 4.0 | 0.0 | 1.0 | 1.0 | 0.0 | 1.0 | 1.0 | 0.0 |
13 | GO:0019344 | cysteine biosynthetic process | 82 | 25.0 | 8.0 | 57.0 | 6.0 | 15.0 | 2.0 | 0.0 | 6.0 | 21.0 | 19.0 | 19.0 | 7.0 | 10.0 | 5.0 | 8.0 | 6.0 | 1.0 | 1.0 | 0.0 | 3.0 | 2.0 | 3.0 | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 |
1 | GO:0004124 | cysteine synthase activity | 29 | 7.0 | 3.0 | 22.0 | 0.0 | 4.0 | 0.0 | 0.0 | 0.0 | 13.0 | 11.0 | 5.0 | 4.0 | 4.0 | 2.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
5 | GO:0006564 | L-serine biosynthetic process | 21 | 16.0 | 8.0 | 5.0 | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 3.0 | 0.0 | 0.0 | 1.0 | 3.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 3.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
8 | GO:0006535 | cysteine biosynthetic process from serine | 20 | 9.0 | 4.0 | 11.0 | 0.0 | 4.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 6.0 | 3.0 | 5.0 | 2.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 |
6 | GO:0006545 | glycine biosynthetic process | 14 | 3.0 | 3.0 | 11.0 | 7.0 | 9.0 | 0.0 | 0.0 | 7.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 5.0 | 0.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 |
2 | GO:0019343 | cysteine biosynthetic process via cystathionine | 9 | 1.0 | 0.0 | 8.0 | 1.0 | 2.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 5.0 | 0.0 | 0.0 | 0.0 | 1.0 | 3.0 | 0.0 | 0.0 | 0.0 | 2.0 | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
9 | GO:0009090 | homoserine biosynthetic process | 8 | 4.0 | 4.0 | 4.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 4.0 | 0.0 | 0.0 | 0.0 | 0.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 |
10 | GO:0070179 | D-serine biosynthetic process | 8 | 0.0 | 0.0 | 8.0 | 6.0 | 6.0 | 4.0 | 0.0 | 6.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
0 | GO:0016260 | selenocysteine biosynthetic process | 6 | 4.0 | 4.0 | 2.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
11 | GO:0019264 | glycine biosynthetic process from serine | 6 | 2.0 | 2.0 | 4.0 | 2.0 | 4.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 |
3 | GO:0019265 | glycine biosynthetic process, by transaminatio... | 4 | 0.0 | 0.0 | 4.0 | 3.0 | 3.0 | 0.0 | 0.0 | 3.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
7 | GO:0071269 | L-homocysteine biosynthetic process | 1 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
4 | GO:0019345 | cysteine biosynthetic process via S-sulfo-L-cy... | 0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |