Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

pombe differences to GO database #2196

Closed
ValWood opened this issue Sep 25, 2018 · 5 comments
Closed

pombe differences to GO database #2196

ValWood opened this issue Sep 25, 2018 · 5 comments
Assignees
@ValWood
Labels
unknowns

Comments

@ValWood
Copy link
Member

ValWood commented Sep 25, 2018 •
edited
Loading

GO term mapper reports:
These 660 identifiers had no non-root annotations:

which is quite different from us:
https://www.pombase.org/gene_subset/non_go_slim_without_bp_annotation

but this is likely to be due to
i) PAINT annotations, and
ii) relaxed slim not the reason. I'm using the PomBAse slim

Since we use the same PAINT inferences for other species I'll go with it but need to look into this
@ValWood
Copy link
Member Author

ValWood commented Sep 25, 2018

These are fine. They have a process annotation, they are not captured by our slim, but they are captured by the less restrictive slim we are using for the paper

Systematic ID Name Product description
SPBC3H7.09 erf2 palmitoyltransferase Erf2
SPAC3F10.07c erf4 palmitoyltransferase complex subunit Erf4
SPBC947.09 hsp3103 ThiJ domain protein, implicated in cellular detoxification
SPAC11D3.13 hsp3104 ThiJ domain protein, implicated in cellular detoxification
SPCC4B3.10c ipk1 inositol 1,3,4,5,6-pentakisphosphate (IP5) kinase
SPBC2F12.15c pfa3 palmitoyltransferase Pfa3 (predicted)
SPBC691.01 pfa5 vacuolar membrane palmitoyltransferase Pfa5 (predicted)
SPAC890.07c rmt1 type I protein arginine N-methyltransferase Rmt1
SPBC12D12.01 sad1 spindle pole body SUN domain protein Sad1
SPBC13G1.07 swf1 palmitoyltransferase Swf1 (predicted)
SPAC26A3.01 sxa1 aspartic protease Sxa1

@ValWood
Copy link
Member Author

ValWood commented Sep 25, 2018

annotated at GO, not in POmBAse

Systematic ID Name
SPAC17A5.16 ftp105
SPAC144.14 klp8
SPBC19F8.04c lcl3
SPAC630.09c mug58
SPAC3C7.09 set8
SPCC584.11c svf1
SPAC18B11.03c
SPAC1F7.10
SPAC23G3.05c
SPAP27G11.12
SPBC16C6.01c
SPBP19A11.07c
SPBPB10D8.06c

@ValWood
Copy link
Member Author

ValWood commented Sep 25, 2018 •
edited
Loading

696-660 diff

prt2 SPBC8E4.02c pho84 repressing sense RNA Prt2
annotated recently

@ValWood
Copy link
Member Author

ValWood commented Sep 25, 2018 •
edited
Loading

check these, annotated by PAINT, but not by us

IMPLICATED I did not think the evidence was strong enough to annotate these

SPCC306.06c big1 ER membrane protein, BIG1 family, implicated in protein glycosylation (predicted)
SPAC17A5.16 ftp105 Golgi localized protein, human HID1 ortholog 3, implicated in vesicle-mediated transport
SPAC1F7.06 hsp3105 ThiJ domain protein, implicated in cellular detoxification
SPAC630.09c mug58 GLYK family kinase of unknown specificity, implicated in nucleotide metabolism (predicted)
SPBP19A11.07c human HID1 ortholog 2, possible Golgi protein (by similarity)
SPAC23G3.05c conserved endomembrane protein, regulator of G-protein signaling (RGS) domain, implicated in signal transduction (predicted)
SPBC19F8.04c lcl3 mitochondrial nuclease Lcl3, implicated in DNA repair (predicted)
SPCC1795.09 yps1 aspartic protease, yapsin family, unknown specificity Yps1
SPAP27G11.12 human HID1 ortholog 1, possible Golgi protein (by similarity)

REPORTED

Difficult ones
SPAC1296.05c lcp1 cyclin L family cyclin
SPCC320.07c mde7 RNA-binding protein Mde7

TELOMERIC truncations
SPAC212.06c DNA helicase in rearranged telomeric region, truncated
SPAC977.04 truncated C terminal region of membrane transporter

HIGH LEVEL ANNOTATION, OR FUNCTION IN PROESS, EXCLUDED FROM SLIM

  • SPAC3A12.02 mitochondrial inorganic diphosphatase (predicted)
    phosphate-containing compound metabolic process
  • SPAC23C11.05 ipp1 inorganic pyrophosphatase Ipp1 (predicted)
  • SPAC18B11.03c N-acetyltransferase (predicted)
    SPAC18B11.03c PAINT annotation "response to drug" geneontology/go-annotation#2250
  • SPAC1F7.10 hydantoin racemase family (predicted)
    nitrogen compound metabolic process (2859/400 have this annotation, it is anything containing Nitrogen!)
    SPCC584.11c svf1 Svf1 family protein, lipocalin superfamily Svf1
    cellular response to oxidative stress
    SPAC144.14 klp8 kinesin-like protein Klp8 microtubule-based movement
    SPBC16C6.01c lysine methyltransferase, human SETD6 ortholog (predicted)
    SPAC3C7.09 set8 lysine methyltransferase Set8, unknown specificity (predicted)

ANNOTATABLE

SPCC4G3.17 hdd1 HD domain protein phosphoric ester hydrolase family (predicted)
pyrimidine deoxyribonucleotide salvage
dUMP biosynthetic process

SPBP35G2.14 puf2 pumilio family RNA-binding protein Puf2

@ValWood ValWood self-assigned this Oct 7, 2018
@ValWood
Copy link
Member Author

ValWood commented Jan 28, 2019

All done

@ValWood ValWood closed this as completed Jan 28, 2019
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@ValWood ValWood

Labels
unknowns
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@ValWood