Difference between revisions of "Talk:Working Group:Sequence Features"
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CHROMOSOME_X TF_binding_site TF_binding_site 4100019 4100026 . - . Feature "WBsf216754" ; TF_ID "WBTranscriptionFactor000126" ; TF_name "CEH-6" | CHROMOSOME_X TF_binding_site TF_binding_site 4100019 4100026 . - . Feature "WBsf216754" ; TF_ID "WBTranscriptionFactor000126" ; TF_name "CEH-6" | ||
CHROMOSOME_X TF_binding_site TF_binding_site 4100019 4100026 . - . Feature "WBsf216755" ; TF_ID "WBTranscriptionFactor000126" ; TF_name "CEH-6" | CHROMOSOME_X TF_binding_site TF_binding_site 4100019 4100026 . - . Feature "WBsf216755" ; TF_ID "WBTranscriptionFactor000126" ; TF_name "CEH-6" | ||
− | Resolved: positions checked and remapped (together with WBsf216756) from the papers' supplemental table 2 - GW | + | Resolved: positions checked and remapped (together with WBsf216756) from the papers' supplemental table 2 - GW - THE REST OF THE LOCATIONS IN THIS PAPER SHOULD BE RECHECKED !!!!!!! |
These two need to be merged. WBsf899549 should be retired as it is incorrect - this is not a TF binding site, it is a regulatory region. | These two need to be merged. WBsf899549 should be retired as it is incorrect - this is not a TF binding site, it is a regulatory region. | ||
CHROMOSOME_X regulatory_region misc_feature 5100882 5100888 . + . Feature "WBsf919622" | CHROMOSOME_X regulatory_region misc_feature 5100882 5100888 . + . Feature "WBsf919622" | ||
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Resolved: WBsf899548 merged into WBsf919626 - GW | Resolved: WBsf899548 merged into WBsf919626 - GW | ||
WBsf047482 cites paper WBPaper00025203 - this has now been merged with paper WBPaper00026601 and should really be updated to this in all 11 Features which use it. | WBsf047482 cites paper WBPaper00025203 - this has now been merged with paper WBPaper00026601 and should really be updated to this in all 11 Features which use it. | ||
− | + | Resolved: changed the paper ID in all 11 Features. - GW | |
These two Features are otherwise nearly identical and should be merged. | These two Features are otherwise nearly identical and should be merged. | ||
+ | WBsf042312 cites paper WBPaper00025051 | ||
CHROMOSOME_X TF_binding_site TF_binding_site 8940207 8940220 . - . Feature "WBsf042312" ; TF_ID "WBTranscriptionFactor000052" ; TF_name "DAF-19" | CHROMOSOME_X TF_binding_site TF_binding_site 8940207 8940220 . - . Feature "WBsf042312" ; TF_ID "WBTranscriptionFactor000052" ; TF_name "DAF-19" | ||
CHROMOSOME_X TF_binding_site TF_binding_site 8940207 8940220 . - . Feature "WBsf047482" ; TF_ID "WBTranscriptionFactor000052" ; TF_name "DAF-19" | CHROMOSOME_X TF_binding_site TF_binding_site 8940207 8940220 . - . Feature "WBsf047482" ; TF_ID "WBTranscriptionFactor000052" ; TF_name "DAF-19" | ||
+ | Resolved: WBsf042312 merged into WBsf047482 - GW | ||
These two need to be merged. WBsf919641 should be retired as it is incorrect - this is a TF binding site, it is not just a binding_site. | These two need to be merged. WBsf919641 should be retired as it is incorrect - this is a TF binding site, it is not just a binding_site. | ||
+ | The gene is probably myo-2 (T18D3.4) not T18D3.14 | ||
CHROMOSOME_X binding_site binding_site 12467733 12467737 . + . Feature "WBsf919641" | CHROMOSOME_X binding_site binding_site 12467733 12467737 . + . Feature "WBsf919641" | ||
CHROMOSOME_X TF_binding_site TF_binding_site 12467733 12467737 . + . Feature "WBsf919607" ; TF_ID "WBTranscriptionFactor000472" ; TF_name "DAF-3" | CHROMOSOME_X TF_binding_site TF_binding_site 12467733 12467737 . + . Feature "WBsf919607" ; TF_ID "WBTranscriptionFactor000472" ; TF_name "DAF-3" |
Latest revision as of 10:20, 23 September 2014
Duplicated Features
These two need to be merged - I suggest WBsf019227 be retired as it is in the opposite sense to its gene. CHROMOSOME_I TF_binding_site TF_binding_site 10245805 10245811 . - . Feature "WBsf019227" ; TF_ID "WBTranscriptionFactor000101" ; TF_name "LAG-1" CHROMOSOME_I TF_binding_site TF_binding_site 10245805 10245811 . + . Feature "WBsf038813" ; TF_ID "WBTranscriptionFactor000101" ; TF_name "LAG-1"
Resolved already - GW
These two need to be merged - I suggest WBsf019221 be retired as it doesn't have the Interaction objects. CHROMOSOME_I TF_binding_site TF_binding_site 10245835 10245841 . + . Feature "WBsf019221" ; TF_ID "WBTranscriptionFactor000101" ; TF_name "LAG-1" CHROMOSOME_I TF_binding_site TF_binding_site 10245835 10245841 . + . Feature "WBsf038814" ; TF_ID "WBTranscriptionFactor000101" ; TF_name "LAG-1"
Resolved: WBsf019221 merged into WBsf038814 - GW
These two need to be merged - no difference between them. The SO_term is wrong - needs to be SO:0000235 CHROMOSOME_II TF_binding_site TF_binding_site 10950131 10950138 . + . Feature "WBsf019124" ; TF_ID "WBTranscriptionFactor000014" ; TF_name "SKN-1" CHROMOSOME_II TF_binding_site TF_binding_site 10950131 10950138 . + . Feature "WBsf019126" ; TF_ID "WBTranscriptionFactor000014" ; TF_name "SKN-1"
Resolved: WBsf019124 merged into WBsf019126 - GW
Two papers - one says this is a MEX-1 recognition elemant and the other says this is a MEX-3 recognition element - are they both right? CHROMOSOME_III binding_site binding_site 4804863 4804877 . - . Feature "WBsf899528" CHROMOSOME_III binding_site binding_site 4804863 4804877 . - . Feature "WBsf899543"
Resolved: WBsf899528 merged into WBsf899543 - GW
Two papers - one says this is a MEX-1 recognition elemant and the other says this is a MEX-3 recognition element - are they both right? CHROMOSOME_III binding_site binding_site 4804911 4804928 . - . Feature "WBsf899526" CHROMOSOME_III binding_site binding_site 4804911 4804928 . - . Feature "WBsf899542"
Resolved: WBsf899526 merged into WBsf899542 - GW
These are from the same paper - one says it is "PUF-8 recognition element (PRE-1)" and the other says it is "PUF-8 recognition element (PRE-2)". Are they both right? CHROMOSOME_III binding_site binding_site 4805138 4805145 . - . Feature "WBsf899537" CHROMOSOME_III binding_site binding_site 4805138 4805145 . - . Feature "WBsf899538"
Resolved: WBsf899537 (PRE-1) was in the wrong position - now correct - GW
These are from the same paper - one says it is "TF LIN-1 binding site S11 in pJW5" and the other is "TF LIN-1 binding site S20 in pJW5" - looks like an error to me - Gary to redo this. CHROMOSOME_III TF_binding_site TF_binding_site 7540351 7540361 . - . Feature "WBsf919592" ; TF_ID "WBTranscriptionFactor000135" ; TF_name "LIN-1" CHROMOSOME_III TF_binding_site TF_binding_site 7540351 7540361 . - . Feature "WBsf919594" ; TF_ID "WBTranscriptionFactor000135" ; TF_name "LIN-1"
Resolved: WBsf919594 was in th ewrong position - now correct - GW
These two need to be merged - I suggest WBsf047654 be retired as it contains less information. CHROMOSOME_III regulatory_region misc_feature 7540972 7540992 . - . Feature "WBsf047654" CHROMOSOME_III regulatory_region misc_feature 7540972 7540992 . - . Feature "WBsf919589"
Resolved: WBsf047654 merged into WBsf919589 - GW
These two need to be merged - they are from different papers. I suggest WBsf047505 be retired as it has an incorrect SO_term - needs to be SO:0000235 CHROMOSOME_IV TF_binding_site TF_binding_site 2306593 2306606 . - . Feature "WBsf047478" ; TF_ID "WBTranscriptionFactor000052" ; TF_name "DAF-19" CHROMOSOME_IV TF_binding_site TF_binding_site 2306593 2306606 . - . Feature "WBsf047505" ; TF_ID "WBTranscriptionFactor000052" ; TF_name "DAF-19"
Resolved: WBsf047505 merged into WBsf047478 - GW
These two need to be merged - they are from different papers. I suggest WBsf019088 be retired as it has an incorrect SO_term - needs to be SO:0000235 CHROMOSOME_V TF_binding_site TF_binding_site 10671938 10671944 . + . Feature "WBsf019088" ; TF_ID "WBTranscriptionFactor000061" ; TF_name "CEH-22" CHROMOSOME_V TF_binding_site TF_binding_site 10671938 10671944 . + . Feature "WBsf919536" ; TF_ID "WBTranscriptionFactor000061" ; TF_name "CEH-22"
Resolved: WBsf019088 merged into WBsf919536 - GW
These three need to be merged. They are identical. The SO_term is wrong - needs to be SO:0000235 CHROMOSOME_V TF_binding_site TF_binding_site 11882353 11882360 . + . Feature "WBsf216760" ; TF_ID "WBTranscriptionFactor000126" ; TF_name "CEH-6" CHROMOSOME_V TF_binding_site TF_binding_site 11882353 11882360 . + . Feature "WBsf216762" ; TF_ID "WBTranscriptionFactor000126" ; TF_name "CEH-6" CHROMOSOME_V TF_binding_site TF_binding_site 11882353 11882360 . + . Feature "WBsf216764" ; TF_ID "WBTranscriptionFactor000126" ; TF_name "CEH-6"
Resolved: Merged WBsf216760 and WBsf216762 into WBsf216764 - GW
These three need to be merged. They are identical. The SO_term is wrong - needs to be SO:0000235 CHROMOSOME_X TF_binding_site TF_binding_site 4100019 4100026 . - . Feature "WBsf216754" ; TF_ID "WBTranscriptionFactor000126" ; TF_name "CEH-6" CHROMOSOME_X TF_binding_site TF_binding_site 4100019 4100026 . - . Feature "WBsf216755" ; TF_ID "WBTranscriptionFactor000126" ; TF_name "CEH-6"
Resolved: positions checked and remapped (together with WBsf216756) from the papers' supplemental table 2 - GW - THE REST OF THE LOCATIONS IN THIS PAPER SHOULD BE RECHECKED !!!!!!!
These two need to be merged. WBsf899549 should be retired as it is incorrect - this is not a TF binding site, it is a regulatory region. CHROMOSOME_X regulatory_region misc_feature 5100882 5100888 . + . Feature "WBsf919622" CHROMOSOME_X TF_binding_site TF_binding_site 5100882 5100888 . + . Feature "WBsf899549"
Resolved: Merged WBsf899549 into WBsf919622 - GW
These two need to be merged. WBsf899545 should be retired as it is incorrect - this is not a TF binding site, it is a regulatory region. CHROMOSOME_X regulatory_region misc_feature 5100919 5100925 . + . Feature "WBsf919623" CHROMOSOME_X TF_binding_site TF_binding_site 5100919 5100925 . + . Feature "WBsf899545"
Resolved: Merged WBsf899545 into WBsf919623 - GW
These two need to be merged. WBsf899547 should be retired as it is incorrect - this is not a TF binding site, it is a regulatory region. CHROMOSOME_X regulatory_region misc_feature 5100970 5100976 . + . Feature "WBsf919625" CHROMOSOME_X TF_binding_site TF_binding_site 5100970 5100976 . + . Feature "WBsf899547"
Resolved: merged WBsf899547 into WBsf919625 - GW
These two need to be merged. WBsf899548 should be retired as it is incorrect - this is not a TF binding site, it is a regulatory region. CHROMOSOME_X regulatory_region misc_feature 5100985 5100991 . + . Feature "WBsf919626" CHROMOSOME_X TF_binding_site TF_binding_site 5100985 5100991 . + . Feature "WBsf899548"
Resolved: WBsf899548 merged into WBsf919626 - GW
WBsf047482 cites paper WBPaper00025203 - this has now been merged with paper WBPaper00026601 and should really be updated to this in all 11 Features which use it.
Resolved: changed the paper ID in all 11 Features. - GW
These two Features are otherwise nearly identical and should be merged. WBsf042312 cites paper WBPaper00025051 CHROMOSOME_X TF_binding_site TF_binding_site 8940207 8940220 . - . Feature "WBsf042312" ; TF_ID "WBTranscriptionFactor000052" ; TF_name "DAF-19" CHROMOSOME_X TF_binding_site TF_binding_site 8940207 8940220 . - . Feature "WBsf047482" ; TF_ID "WBTranscriptionFactor000052" ; TF_name "DAF-19"
Resolved: WBsf042312 merged into WBsf047482 - GW
These two need to be merged. WBsf919641 should be retired as it is incorrect - this is a TF binding site, it is not just a binding_site. The gene is probably myo-2 (T18D3.4) not T18D3.14 CHROMOSOME_X binding_site binding_site 12467733 12467737 . + . Feature "WBsf919641" CHROMOSOME_X TF_binding_site TF_binding_site 12467733 12467737 . + . Feature "WBsf919607" ; TF_ID "WBTranscriptionFactor000472" ; TF_name "DAF-3"