咖啡会友第二弹，基于PWM的 DNA 转录因子结合位点预测等TRANSFAC相关问题的在线答疑
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微信公众号: geneXplain
该视频是 2023 年 2 月 7 日举行的“与 TRANSFAC 的第二次茶歇”在线答疑的记录。
该活动由 geneXplain GmbH 首席执行官 Alexander Kel 博士主持。
这一系列名为“与 TRANSFAC 的茶歇”的周期性活动的目的是为我们的听众提供有关应用生物信息学领域的问题的答案。
您可以在 https://genexplain.com/ask
上找到有关“与 TRANSFAC 相约茶聚”的更多信息
本次会议中解决的问题列表及其时间代码：
04:10 TFBS prediction in DNA based on positional weight matrices
06:12 How to define the cutoffs for binding sites scores
10:51 In calculating FP and FN you need to know the true binding sites. How are they determined?
23:10 I have some questions about my data derived from the TRANSFAC 2012 professional matrices. 1) Some of the genes of interest have binding sites for IRF (without further specification of the subtype), STAT (again, without further specification of the subtype). Can you explain what this means? 2) Some other genes have binding sites for STAT1STAT1 - does this mean STAT1 dimer, also known as the GAS element?
49:22 I am interested to find out what TFs, promoter & enhancer regions, and epigenetic signatures are relevant for the regulation of specific genes in rat hippocampal pyramidal and inhibitory neurons. I know this is not an easy task, and needs not only a bioinformatic but also an experimental approach. I am not aware how transcriptome (RNAseq) and epigenetic (ATAC-seq) data are integrated in the TRANSFAC platform and whether TRANSFAC could help in refining this.
该视频是 2023 年 2 月 7 日举行的“与 TRANSFAC 的第二次茶歇”在线答疑的记录。
该活动由 geneXplain GmbH 首席执行官 Alexander Kel 博士主持。
这一系列名为“与 TRANSFAC 的茶歇”的周期性活动的目的是为我们的听众提供有关应用生物信息学领域的问题的答案。
您可以在 https://genexplain.com/ask
上找到有关“与 TRANSFAC 相约茶聚”的更多信息
本次会议中解决的问题列表及其时间代码：
04:10 TFBS prediction in DNA based on positional weight matrices
06:12 How to define the cutoffs for binding sites scores
10:51 In calculating FP and FN you need to know the true binding sites. How are they determined?
23:10 I have some questions about my data derived from the TRANSFAC 2012 professional matrices. 1) Some of the genes of interest have binding sites for IRF (without further specification of the subtype), STAT (again, without further specification of the subtype). Can you explain what this means? 2) Some other genes have binding sites for STAT1STAT1 - does this mean STAT1 dimer, also known as the GAS element?
49:22 I am interested to find out what TFs, promoter & enhancer regions, and epigenetic signatures are relevant for the regulation of specific genes in rat hippocampal pyramidal and inhibitory neurons. I know this is not an easy task, and needs not only a bioinformatic but also an experimental approach. I am not aware how transcriptome (RNAseq) and epigenetic (ATAC-seq) data are integrated in the TRANSFAC platform and whether TRANSFAC could help in refining this.
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