Merles data

[ValWood]

February 26 for the online version.

These are the tasks:

• TASK 1 URLs on publication page
  1 Strains
  is now available as a set: https://yeast.nig.ac.jp/yeast/fy/StrainSetAllItemsList.jsf set “FYS8” to get to the page of all strain sets but that has the order button or for a list of all strain included in the set go directly to “https://yeast.nig.ac.jp/yeast/fy/StrainSetIndividualList.jsf?id=8

2. Link to tool
3. Accessions for datasets (just project, not individual)

• TASK 2 URL on gene pages, deep links (to tool) on TF pages (need IDs)
  @kimrutherford

• TASK 3 Browser datasets (CHipSeq) ~82x4?
  @PCarme to prepare metadata spreadsheeet
  @merle will sned lighter date (check status)

• TASK 4 Browser track of HOTS

• TASK 5 BIOGRID stype interaction forIP/Mass spec
  Merle will send 2 list 2 lists
  High confidence 2 Fold enriched with high alue cut-off
  We need to look at these list to decide which cut-off to proceed with

• TASK 6 GO promoter targets and TF annotations
  @ValWood will create GO -> target gene GO annotation tsv sile (use DNA binding term)
  @ValWood will create GO EXP annotation to TF for the transcription factors

• TASK 7 Artemis
  @ValWood to convert from inferred to published

• TASK 8 ? network, similarity scores based on interactions (what was this)

• TASK 9 Motif list , add to website
  @PCarme add to website

• TASK 10 @kimrutherford rerun marks code to update the TF motif browser track

• TASK 11 Small scale send Canto session to Merle
  Nattou Complex etc

[ValWood]

TASK 6
I made some progress creating the GO-GAF using Chat-GPT and some ancient perl knowledge.

Converted file:
Ace2,SPAC343.13
Ace2,SPAC343.20
Ace2,SPAPYUG7.03c
Ace2,SPNCRNA.1246
Ace2,SPCC1442.07c
Ace2,SPCC18.01c
Cdc10,SPAP14E8.02
Cdc10,SPAC17H9.20

Into a GAF (4294 rows)

GAF_Needs_sys.csv

I still need to:

1. Fix the text "Systemtic_id" in column 2 for the published genes which were referenced by primary names
2. remove all of the "null" field text
3. Fix the ENSEMBL RNA IDS
4. Fix the PMID:XXXXXXX

[ValWood]

• TASK 7

changed these inferred to published:
Systematic ID Gene name Product description
SPAC105.03c dal81 DNA-binding transcription factor
SPAC11D3.07c toe4 DNA-binding transcription factor, zf-fungal binuclear cluster type
SPAC11D3.11c DNA-binding transcription factor, zn(2)-C6 fungal-type, truncated
SPAC11D3.17 DNA-binding transcription factor, zf-fungal binuclear cluster type
SPAC1327.01c DNA-binding transcription factor, zf-fungal binuclear cluster type
SPAC1F7.11c DNA-binding transcription factor, zf-fungal binuclear cluster type
SPAC25B8.11 DNA-binding transcription factor
SPAC2H10.01 DNA-binding transcription factor, zf-fungal binuclear cluster type
SPAC3C7.04 DNA-binding transcription factor
SPAC3F10.12c DNA-binding transcription factor
SPAC3H8.08c DNA-binding transcription factor
SPBC1652.01 stb3 DNA-binding transcription factor Stb3
SPBC16G5.16 ntu1 DNA-binding transcription factor, zf-fungal binuclear cluster type
SPBC16G5.17 DNA-binding transcription factor, zf-fungal binuclear cluster type
SPBC1773.12 DNA-binding transcription factor, zf-fungal binuclear cluster type
SPBC1773.16c DNA-binding transcription factor, zf-fungal binuclear cluster type
SPBC530.08 ntu2 DNA-binding transcription factor, membrane-tethered
SPBC530.11c DNA-binding transcription factor, zf-fungal binuclear cluster type
SPBC56F2.05c DNA-binding transcription factor
SPCC18.03 shuttle craft like transcriptional repressor/ubiquitin-protein ligase E3
SPCC757.04 DNA-binding transcription factor
SPCC777.02 DNA-binding transcription factor
SPCC965.10 DNA-binding transcription factor