webgestalt

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Cristian Fiorucci, Yuxing Liao2

Mar 24

Visualization error

Hi Cristian, Could you share an example link? Thanks. Yuxing On Fri, Mar 24, 2023 at 3:25 AM Cristian

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Visualization error

Hi Cristian, Could you share an example link? Thanks. Yuxing On Fri, Mar 24, 2023 at 3:25 AM Cristian

Mar 24

Cristian Fiorucci, Yuxing Liao3

Mar 16

Different significance with ORA and GSEA

Thank you for your help! Il giorno mercoledì 15 marzo 2023 alle 21:22:19 UTC+1 yuxin...@gmail.com ha

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Different significance with ORA and GSEA

Thank you for your help! Il giorno mercoledì 15 marzo 2023 alle 21:22:19 UTC+1 yuxin...@gmail.com ha

Mar 16

Letoto H, John Elizarraras6

Mar 15

The order of the genes does not matter, but they should all have a score. Happy to help, and if you

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The order of the genes does not matter, but they should all have a score. Happy to help, and if you

Mar 15

Juan Manuel Luque, Yuxing Liao2

Mar 13

To change colors of Bar chart

Hi Juan, Sorry, your email went to spam. For the question, unfortunately you can't on the website

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To change colors of Bar chart

Hi Juan, Sorry, your email went to spam. For the question, unfortunately you can't on the website

Mar 13

Mario Ezquerra, Yuxing Liao2

Feb 16

Uniprot protein ID with phosphosites annotation format?

Hi Mario, There are 4 ID types, and hovering over the options after a while shows a few examples. You

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Uniprot protein ID with phosphosites annotation format?

Hi Mario, There are 4 ID types, and hovering over the options after a while shows a few examples. You

Feb 16

alessio colantoni, John Elizarraras3

Feb 15

Organism not found

Dear John, now it is working. Thank you so much. Best regards, Alessio Il giorno martedì 14 febbraio

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Organism not found

Dear John, now it is working. Thank you so much. Best regards, Alessio Il giorno martedì 14 febbraio

Feb 15

Feb 9

custom analysis on WebGestaltR

Hello I am trying to perform an analysis using a non-model organism. I have generated the files and

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custom analysis on WebGestaltR

Hello I am trying to perform an analysis using a non-model organism. I have generated the files and

Feb 9

Vincent Lynch, Yuxing Liao5

Jan 31

gmt file format Q

Thanks, that I get but I still have a couple questions: 1) Why do the P-values change when the number

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gmt file format Q

Thanks, that I get but I still have a couple questions: 1) Why do the P-values change when the number

Jan 31

SJ Koppes, Yuxing Liao2

Jan 10

The majority of the input gene list does not have two columns

Hi Sascha, Please use tabs to separate the columns. I think that is the problem. Yuxing On Tue, Jan 3

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The majority of the input gene list does not have two columns

Hi Sascha, Please use tabs to separate the columns. I think that is the problem. Yuxing On Tue, Jan 3

Jan 10

12/15/22

miRNA analysis protocol

In some paper, i saw that a mirna-target mRNA network was created using this program. But i don't

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miRNA analysis protocol

In some paper, i saw that a mirna-target mRNA network was created using this program. But i don't

12/15/22

MARCEL LUCAS SÁNCHEZ, Yuxing Liao4

11/17/22

Incorrect number of dimensions

Hi Marcel, Using your list 2 as input and list 1 as reference gives a different error for the OMIM

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Incorrect number of dimensions

Hi Marcel, Using your list 2 as input and list 1 as reference gives a different error for the OMIM

11/17/22

Lisa, Yuxing Liao2

11/11/22

Hi Lisa, Sorry, I am afraid that I am not familiar with the network analysis part to answer your

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Hi Lisa, Sorry, I am afraid that I am not familiar with the network analysis part to answer your

11/11/22

Mehdi B, Yuxing Liao2

10/22/22

GSEA on small gene panels - nanostring

Hi Mehdi, I am not sure I understand your question correctly. But check this below. https://software.

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GSEA on small gene panels - nanostring

Hi Mehdi, I am not sure I understand your question correctly. But check this below. https://software.

10/22/22

Samah Al Segehy, Yuxing Liao3

10/20/22

WebGestalt - LogFC

Thank so much for your response. I really do appreciate it. On Thursday, October 20, 2022 at 3:36:50

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WebGestalt - LogFC

Thank so much for your response. I really do appreciate it. On Thursday, October 20, 2022 at 3:36:50

10/20/22

Andre Gerber, Yuxing Liao2

10/2/22

Hi Andre, FDR zero just means it is smaller than 2.2e-16. See double.eps in https://stat.ethz.ch/R-

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Hi Andre, FDR zero just means it is smaller than 2.2e-16. See double.eps in https://stat.ethz.ch/R-

10/2/22

Vincent Lynch, Yuxing Liao3

9/23/22

Error with minimum number of genes for a category?

Ah, thanks. I misinterpreted that setting! On Sep 21, 2022, at 4:40 PM, Yuxing Liao <yuxingliao@

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Error with minimum number of genes for a category?

Ah, thanks. I misinterpreted that setting! On Sep 21, 2022, at 4:40 PM, Yuxing Liao <yuxingliao@

9/23/22

Niranjan Shirgaonkar2

9/23/22

Too few or too many genes!

The analysis worked when I put the minimum number of genes for a category = 3 On Friday, 23 September

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Too few or too many genes!

The analysis worked when I put the minimum number of genes for a category = 3 On Friday, 23 September

9/23/22

Etay Livne, Yuxing Liao2

9/21/22

Explanation of redundancy reduction methods

Hi Etay, The redundancy reduction is designed to cluster enriched gene sets that share great overlaps

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Explanation of redundancy reduction methods

Hi Etay, The redundancy reduction is designed to cluster enriched gene sets that share great overlaps

9/21/22

Anirban Roy, Yuxing Liao2

8/17/22

Regarding GSEA analysis

Hi Anirban, 1. I would recommend log2 transformed values, especially if you have a few ones with very

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Regarding GSEA analysis

Hi Anirban, 1. I would recommend log2 transformed values, especially if you have a few ones with very

8/17/22

Teka Khan, Yuxing Liao2

8/17/22

ERROR: The format of the uploaded ranked list is incorrect. Please make sure the file contains two column of gene IDs and scores.

Could you check other answered questions about this? or attach an example input file? On Fri, Jul 29,

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ERROR: The format of the uploaded ranked list is incorrect. Please make sure the file contains two column of gene IDs and scores.

Could you check other answered questions about this? or attach an example input file? On Fri, Jul 29,

8/17/22

Severin Uebbing, Yuxing Liao3

8/17/22

Two overlapping gene sets - duplicate enrichment?

Hi Severin, I am not sure about the degree of significance. I think if you check the number of

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Two overlapping gene sets - duplicate enrichment?

Hi Severin, I am not sure about the degree of significance. I think if you check the number of

8/17/22

Agnese Giovannetti, Yuxing Liao2

8/12/22

Adjusted p-values for ORA analysis

Hi Agnese, I think it is likely because you do not have p-values for all gene sets to compare. For

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Adjusted p-values for ORA analysis

Hi Agnese, I think it is likely because you do not have p-values for all gene sets to compare. For

8/12/22

7/28/22

Re: [webgestalt] Problem with rnk file for GSEA analysis

Hi Andrea, It is just a text file with two tab-separated columns. Have you tried to paste it in the

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Re: [webgestalt] Problem with rnk file for GSEA analysis

Hi Andrea, It is just a text file with two tab-separated columns. Have you tried to paste it in the

7/28/22

Vipul Batra, Yuxing Liao2

7/28/22

Different output same input-DOSI

Hi, could you provide the two input lists you used? On Tue, Jul 5, 2022 at 5:37 AM Vipul Batra <

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Different output same input-DOSI

Hi, could you provide the two input lists you used? On Tue, Jul 5, 2022 at 5:37 AM Vipul Batra <

7/28/22

Pengmin Wang, Yuxing Liao2

7/28/22

what's the data source of webgestaltR?

Hi Pengmin, The detailed information and date is in the panel on the right side. But it is definitely

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what's the data source of webgestaltR?

Hi Pengmin, The detailed information and date is in the panel on the right side. But it is definitely

7/28/22

Alex0520Covid Chin, Yuxing Liao2

7/28/22

Which FDR method did you put in ORA?

Hi Alex, There is an option for it in the expandable "advanced parameters" section in the

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Which FDR method did you put in ORA?

Hi Alex, There is an option for it in the expandable "advanced parameters" section in the

7/28/22

Andrea Ghiroldi2

7/12/22

Problem with the .rnk file for GSEA

Il giorno martedì 12 luglio 2022 alle 17:15:36 UTC+2 Andrea Ghiroldi ha scritto: Hi, I tried to

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Problem with the .rnk file for GSEA

Il giorno martedì 12 luglio 2022 alle 17:15:36 UTC+2 Andrea Ghiroldi ha scritto: Hi, I tried to

7/12/22

6/9/22

Kinase Target database

Hi, May I learn more about the reference phosphosite used in the Kinase target database. Is it based

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Kinase Target database

Hi, May I learn more about the reference phosphosite used in the Kinase target database. Is it based

6/9/22

ilian atanassov

5/6/22

How to interpret non-reported gene sets

Dear Webgestalt community, I would like to have your feedback regarding the interpretation of the

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How to interpret non-reported gene sets

Dear Webgestalt community, I would like to have your feedback regarding the interpretation of the

5/6/22

Angeli Ambayya, … ilian atanassov3

5/6/22

Enrichment plot interpretation

Hi Angeli, I the first 10 min of this video rather useful, https://www.youtube.com/watch?v=

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Enrichment plot interpretation

Hi Angeli, I the first 10 min of this video rather useful, https://www.youtube.com/watch?v=

5/6/22

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