Review signaling pathway annotations

[hattrill]

Task: check consisitency of signaling pathway GO annotation and pathway groups.

Make changes/disputes to make the two match. For all but Toll signaling, we have unique terms mapped to each pathway group. (Have requested a new term for Toll signaling spz processing/zymogen cascade, so this should get resolved)

Review sheet

For each pathway:

1. download the genes from the pathway page and for the corresponding term in FlyBase (exact term only)
2. In QuickGO query with GO term and select taxid:7227 - download tsv. Then select only on experimentally evidenced terms and download tsv.
3. Paste these into a tab on the review sheet and compare gene lists: venny is good for this as can compare the 4 sets at the same time
4. Add summary of results to 'Summary' tab on review sheet.
5. Where any differences arise, check and fix.

[hattrill]

Reviewed? Tick off sub-group when reviewed (ie in google sheet), only tick parent when all issues are resolved.

• [x] Activin Signaling Pathway (ACT-SMAD2)
• [x] Activin Signaling Pathway Core Components (ACT-C)
• [x] Negative Regulators of Activin Signaling Pathway (ACT-N)
• [x] Positive Regulators of Activin Signaling Pathway (ACT-P)
• [ ] BMP Signaling Pathway (BMP-MAD)
• [x] BMP Signaling Pathway Core Components (BMP-C)
• [x] Negative Regulators of BMP Signaling Pathway (BMP-N)
• [x] Positive Regulators of BMP Signaling Pathway (BMP-P)
• [x] EGFR Signaling Pathway (EGFR-RTK)
• [x] EGFR Ligand Production (EGF-PRO)
• [x] EGFR Signaling Pathway Core Components (EGFR-C)
• [x] Negative Regulators of EGFR Signaling Pathway (EGFR-N)
• [x] Positive Regulators of EGFR Signaling Pathway (EGFR-P)
• [x] FGFR Signaling Pathway (FGFR)
• [x] FGFR Signaling Pathway Core Components (FGFR-C)
• [x] Negative Regulators of FGFR Signaling Pathway (FGFR-N)
• [x] Positive Regulators of FGFR Signaling Pathway (FGFR-P)
• [ ] Hedgehog Signaling Pathway (HH-SMO)
• [x] Hedgehog Production (HH-PRO)
• [x] Hedgehog Signaling Pathway Core Components (HH-SMOC)
• [x] Negative Regulators of Hedgehog Signaling Pathway (HH-SMON)
• [x] Positive Regulators of Hedgehog Signaling Pathway (HH-SMOP)
• [ ] Hippo Signaling Pathway (SWH)
• [x] Hippo Signaling Pathway Core Components (SWH-C)
• [x] Negative Regulators of Hippo Signaling Pathway (SWH-N)
• [x] Positive Regulators of Hippo Signaling Pathway (SWH-P)
• [ ] Imd Signaling Pathway (IMD)
• [x] Imd Signaling Pathway Core Components (IMD-C)
• [x] Negative Regulators of Imd Signaling Pathway (IMD-N)
• [x] Positive Regulators of Imd Signaling Pathway (IMD-P)
• [ ] Insulin-like Receptor Signaling Pathway (INS)
• [x] Insulin-like Receptor Signaling Pathway Core Components (INS-C)
• [x] Negative Regulators of Insulin-like Receptor Signaling Pathway (INS-N)
• [x] Positive Regulators of Insulin-like Receptor Signaling Pathway (INS-P)
• [ ] JAK-STAT Signaling Pathway (JAKSTAT)
• [x] JAK-STAT Signaling Pathway Core Components (JAKSTAT-C)
• [x] Negative Regulators of JAK-STAT Signaling Pathway (JAKSTAT-N)
• [x] Positive Regulators of JAK-STAT Signaling Pathway (JAKSTAT-P)
• [ ] Notch Signaling Pathway (NTCH)
• [x] Negative Regulators of Notch Signaling Pathway (NTCH-N)
• [x] Notch Signaling Pathway Core Components (NTCH-C)
• [x] Positive Regulators of Notch Signaling Pathway (NTCH-P)
• [x] Pvr Signaling Pathway (PVR-RTK)
• [x] Negative Regulators of Pvr Signaling Pathway (PVR-N)
• [x] Positive Regulators of Pvr Signaling Pathway (PVR-P)
• [x] Pvr Signaling Pathway Core Components (PVR-C)
• [x] Sevenless Signaling Pathway (SEVL)
• [x] Negative Regulators of Sevenless Signaling Pathway (SEVL-N)
• [x] Positive Regulators of Sevenless Signaling Pathway (SEVL-P)
• [x] Sevenless Signaling Pathway Core Components (SEVL-C)
• [ ] TNF&agr;-Eiger Signaling Pathway (TNF)
• [x] Negative Regulators of TNF&agr;-Eiger Signaling Pathway (TNF-N)
• [x] Positive Regulators of TNF&agr;-Eiger Signaling Pathway (TNF-P)
• [x] TNF&agr;-Eiger Signaling Pathway Core Components (TNF-C)
• [x] Toll Signaling Pathway (TL-CAN)
• [x] Extracellular Spatzle Activating Pathway Core Components (TL-SPZC)
• [x] Negative Regulators of Spatzle Activating Pathway (TL-SPZN)
• [x] Negative Regulators of Toll-NF-&kgr;B Signaling Pathway (TL-NFN)
• [x] Positive Regulators of Toll-NF-&kgr;B Signaling Pathway (TL-NFP)
• [x] Toll-NF-&kgr;B Signaling Pathway Core Components (TL-NFC)
• [x] Torso Signaling Pathway (TORS)
• [x] Negative Regulators of Torso Signaling Pathway (TORS-N)
• [x] Positive Regulators of Torso Signaling Pathway (TORS-P)
• [x] Torso Signaling Pathway Core Components (TORS-C)
• [ ] Wnt-TCF Signaling Pathway (WNT-TCF)
• [x] Negative Regulators of Wnt-TCF Signaling Pathway (WNT-TCFN)
• [x] Positive Regulators of Wnt-TCF Signaling Pathway (WNT-TCFP)
• [x] Wnt-TCF Signaling Pathway Core Components (WNT-TCFC)
• [x] Wnt Production (WNT-PRO)

[hattrill]

hi @gantonazzo do you want to meet tomorrow at 10am and spend a couple of hours finishing this off together?

[gantonazzo]

hi @gantonazzo do you want to meet tomorrow at 10am and spend a couple of hours finishing this off together?

Sure, sounds good

[hattrill]

• [ ] Make mass Notch ticket for KW and InterPro
• [ ] reannotate rumi to glycosylation term with target Notch?
• [x] cnk - insulin pathway or not?
• [ ] check ILPs
• [x] Reannotate components of "Toll receptor ligand protein activation cascade" and regulators after _04 load