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Transcription Factor Targets? #79

Closed dbolser closed 10 months ago

dbolser commented 10 months ago

Hi, I went from here: https://maayanlab.cloud/Harmonizome/search?q=Transcription%20Factor%20Targets&t=dataset

to here: https://maayanlab.cloud/Harmonizome/dataset/CHEA+Transcription+Factor+Targets

to here: https://pubmed.ncbi.nlm.nih.gov/20709693/

to here: http://amp.pharm.mssm.edu/lib/chea.jsp

but found myself here: https://maayanlab.cloud/sigcom-lincs/#/SignatureSearch/UpDown

Do you provide Transcription Factor Targets, or is the redirect a false positive?

Many thanks, Dan.

AviMaayan commented 10 months ago

Hi @dbolser the redirect for http://amp.pharm.mssm.edu/lib/chea.jsp should go to https://maayanlab.cloud/chea3/. Thank you for letting us know about this issue.

dbolser commented 10 months ago

Thanks for the quick reply!

On Thu, 2 Nov 2023, 17:05 AviMaayan, @.***> wrote:

Hi @dbolser https://github.com/dbolser the redirect for http://amp.pharm.mssm.edu/lib/chea.jsp should go to https://maayanlab.cloud/chea3/. Thank you for letting us know about this issue.

— Reply to this email directly, view it on GitHub https://github.com/MaayanLab/sigcom-lincs/issues/79#issuecomment-1791135924, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAA7NE2FE777OOGQM7IJBCLYCPHHHAVCNFSM6AAAAAA63HAHMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJRGEZTKOJSGQ . You are receiving this because you were mentioned.Message ID: @.***>

u8sand commented 10 months ago

Done

dbolser commented 10 months ago

Sorry for the basic question, but is there a simple tf / gene association file?

On Thu, 2 Nov 2023, 19:18 Dan Bolser, @.***> wrote:

Thanks for the quick reply!

On Thu, 2 Nov 2023, 17:05 AviMaayan, @.***> wrote:

Hi @dbolser https://github.com/dbolser the redirect for http://amp.pharm.mssm.edu/lib/chea.jsp should go to https://maayanlab.cloud/chea3/. Thank you for letting us know about this issue.

— Reply to this email directly, view it on GitHub https://github.com/MaayanLab/sigcom-lincs/issues/79#issuecomment-1791135924, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAA7NE2FE777OOGQM7IJBCLYCPHHHAVCNFSM6AAAAAA63HAHMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJRGEZTKOJSGQ . You are receiving this because you were mentioned.Message ID: @.***>

AviMaayan commented 10 months ago

No. This is because we have ~18M tf/gene associations under "Download" section here: https://maayanlab.cloud/chea3/. If you want to know the TFs upstream of a specific gene, you can try: https://maayanlab.cloud/Enrichr/#find. If you want to know the targets for a specific TF, you can try: https://maayanlab.cloud/Enrichr/#metadata

dbolser commented 10 months ago

Great! Where can I read more about the 18 million?

On Thu, 2 Nov 2023, 19:32 AviMaayan, @.***> wrote:

No. This is because we have ~18M tf/gene associations under "Download" here. If you want to know TF upstream of a specific gene, you can try: https://maayanlab.cloud/Enrichr/#find. If you want to know the targets for a specific TF, you can try: https://maayanlab.cloud/Enrichr/#metadata

— Reply to this email directly, view it on GitHub https://github.com/MaayanLab/sigcom-lincs/issues/79#issuecomment-1791427977, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAA7NE2ISE5AX3DV3V73P3LYCPYLJAVCNFSM6AAAAAA63HAHMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJRGQZDOOJXG4 . You are receiving this because you were mentioned.Message ID: @.***>

AviMaayan commented 10 months ago

Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, Jagodnik KM, Kropiwnicki E, Wang Z, Ma'ayan A. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. 2019 Jul 2;47(W1):W212-W224. doi: 10.1093/nar/gkz446. PMID: 31114921; PMCID: PMC6602523.