咖啡时间(1) 在线解答是否可直接用基因序列检索转录因子结合位点
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微信公众号: geneXplain
该视频是 2023 年 1 月 17 日举行的“TRANSFAC 在线Q & A, 与Kel博士的第一次茶歇”现场会议的记录。
该活动由 geneXplain GmbH CEO Alexander Kel 博士主持。
这一系列名为“与 Kel 博士的茶歇”是从2023年开始geneXplain 推出的周期性活动，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 上找到更多相关信息
本次会议中解决的问题列表：
How can I start a TRANSFAC bioinformatics analysis? What types of data do I need?
What is the significance of a transcription factor binding site on plus or minus strand of the gene?
New transcription factors - do you survey those all the time? How many targets are necessary for inclusion of one (creation of a matrix) in the program?
What advantages does TRANSFAC have over the HOCOMOCO and JASPAR databases?
Regarding TF binding analysis: even after we get a putative motif for TFs, how many TF could possibly bind at a single site on the genome, depending on a significance cut-off, I find TF binding sites from 2-3 to almost 40-50 at the same location. How do we filter the noise or get accurate results?
Is it possible to use directly gene sequences to search TFBS? For example sequences from Ensembl database? FASTA file?
Either on + strand, or on - strand, one should read the binding site from 5' end to 3' end, is it correct?
Can a gene have two active promoters and corresponding TSS in the same cell?
In order to investigate how much a genetic mutation could affect a TF binding site, is it possible that such a mutation could affect multiple TFs binding at that region? Would it be advisable to focus only on TFs based on their binding score?
The co-occurrence of TFs proposed by TRANSFAC is based on the knowledge coming from different experiments, so what are the chances of co-occurrence actually?
该视频是 2023 年 1 月 17 日举行的“TRANSFAC 在线Q & A, 与Kel博士的第一次茶歇”现场会议的记录。
该活动由 geneXplain GmbH CEO Alexander Kel 博士主持。
这一系列名为“与 Kel 博士的茶歇”是从2023年开始geneXplain 推出的周期性活动，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 上找到更多相关信息
本次会议中解决的问题列表：
How can I start a TRANSFAC bioinformatics analysis? What types of data do I need?
What is the significance of a transcription factor binding site on plus or minus strand of the gene?
New transcription factors - do you survey those all the time? How many targets are necessary for inclusion of one (creation of a matrix) in the program?
What advantages does TRANSFAC have over the HOCOMOCO and JASPAR databases?
Regarding TF binding analysis: even after we get a putative motif for TFs, how many TF could possibly bind at a single site on the genome, depending on a significance cut-off, I find TF binding sites from 2-3 to almost 40-50 at the same location. How do we filter the noise or get accurate results?
Is it possible to use directly gene sequences to search TFBS? For example sequences from Ensembl database? FASTA file?
Either on + strand, or on - strand, one should read the binding site from 5' end to 3' end, is it correct?
Can a gene have two active promoters and corresponding TSS in the same cell?
In order to investigate how much a genetic mutation could affect a TF binding site, is it possible that such a mutation could affect multiple TFs binding at that region? Would it be advisable to focus only on TFs based on their binding score?
The co-occurrence of TFs proposed by TRANSFAC is based on the knowledge coming from different experiments, so what are the chances of co-occurrence actually?
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