This looks like a very exciting competition but I have trouble understanding the data and the task. Starting the thread that will hopefully lead me to be able to explain it to my 5yo daughter :)
\n\n\nFollowing the central dogma of molecular biology: DNA --> RNA-->Protein, your task is as follows:
\n
\n For the Multiome samples: given chromatin accessibility, predict gene expression.
\n For the CITEseq samples: given gene expression, predict protein levels.
Let's start with this one. My understanding it that there is a process going on in cells that starts with DNA, then creates RNA, and ultimately creates proteins. When we look at a specific cell at a specific point in time, I understand that we will see a snapshot of each of them (DNA/RNA/Protein) expressed in some units as a vector. The goal will be to predict one vector based on another vector.
\nConfused about:
\nto be continued
", "messages": [ { "id": "1918825", "postDate": "08/29/2022 21:56:01", "content": "This looks like a very exciting competition but I have trouble understanding the data and the task. Starting the thread that will hopefully lead me to be able to explain it to my 5yo daughter :)
\n\n\nFollowing the central dogma of molecular biology: DNA --> RNA-->Protein, your task is as follows:
\n
\n For the Multiome samples: given chromatin accessibility, predict gene expression.
\n For the CITEseq samples: given gene expression, predict protein levels.
Let's start with this one. My understanding it that there is a process going on in cells that starts with DNA, then creates RNA, and ultimately creates proteins. When we look at a specific cell at a specific point in time, I understand that we will see a snapshot of each of them (DNA/RNA/Protein) expressed in some units as a vector. The goal will be to predict one vector based on another vector.
\nConfused about:
\nto be continued
", "rawMarkdown": "This looks like a very exciting competition but I have trouble understanding the data and the task. Starting the thread that will hopefully lead me to be able to explain it to my 5yo daughter :) \n\n> Following the central dogma of molecular biology: DNA --> RNA-->Protein, your task is as follows:\n> For the Multiome samples: given chromatin accessibility, predict gene expression.\n> For the CITEseq samples: given gene expression, predict protein levels.\n\nLet's start with this one. My understanding it that there is a process going on in cells that starts with DNA, then creates RNA, and ultimately creates proteins. When we look at a specific cell at a specific point in time, I understand that we will see a snapshot of each of them (DNA/RNA/Protein) expressed in some units as a vector. The goal will be to predict one vector based on another vector. \n\n**Confused about**: \n- according to [this video](https://www.youtube.com/watch?v=whV_CkKT7F0) *gene expression* is a combination of transcription (DNA -> mRNA) and translation (mRNA -> Protein) but in this context it seems to be equal to *RNA*? \n- why can't we see the entire DNA and only a snapshot of it at a point in time? \n- what are the units in which we measure DNA/RNA/Proteins?\n\n*to be continued*", "votes": null }, { "id": "1918935", "postDate": "08/30/2022 02:02:21", "content": "Here is a start
\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/346888
To my knowledge,
\naccording to this video gene expression is a combination of transcription (DNA -> mRNA) and translation (mRNA -> Protein) but in this context it seems to be equal to RNA?
\nYes, RNA is equal to messenger RNA (mRNA) in this context.
why can't we see the entire DNA and only a snapshot of it at a point in time?
\nI assume that is because the measurement process, which is composed of several steps like DNA/RNA extraction from cells and mixing with chemical reagent etc., is needed. So while this competition seems like a time-series competition, the time stamp is descrete.
what are the units in which we measure DNA/RNA/Proteins?
\nThe extracted DNA/RNA are fragmented and the nucleotides are sequenced, then each fragment is mapped onto the reference genome according the sequence, and then the fragments counted up in every gene region are finally recorded as the DNA/RNA count. Even regarding the protein measurment, since this competition utilizes the CITE-seq technology, each surface proteins are tagged with synthesized nucleotides and are measured in the same way as above. So the unit is none since the measurement is the number of fragments, I guess. This video might be helpful.
I am glad if you find this helpful.
", "rawMarkdown": "To my knowledge,\n\n- *according to this video gene expression is a combination of transcription (DNA -> mRNA) and translation (mRNA -> Protein) but in this context it seems to be equal to RNA?*\nYes, RNA is equal to messenger RNA (mRNA) in this context.\n\n- *why can't we see the entire DNA and only a snapshot of it at a point in time?*\nI assume that is because the measurement process, which is composed of several steps like DNA/RNA extraction from cells and mixing with chemical reagent etc., is needed. So while this competition seems like a time-series competition, the time stamp is descrete.\n\n- *what are the units in which we measure DNA/RNA/Proteins?*\nThe extracted DNA/RNA are fragmented and the nucleotides are sequenced, then each fragment is mapped onto the reference genome according the sequence, and then the fragments counted up in every gene region are finally recorded as the DNA/RNA count. Even regarding the protein measurment, since this competition utilizes the CITE-seq technology, each surface proteins are tagged with synthesized nucleotides and are measured in the same way as above. So the unit is none since the measurement is the number of fragments, I guess. This [video](youtube.com/watch?v=hWWkpe4Ewgo) might be helpful.\n\nI am glad if you find this helpful.", "votes": null }, { "id": "1919194", "postDate": "08/30/2022 07:41:17", "content": "Nice to meet you,Chis.I learned a lot from you in default prediction competition.
", "rawMarkdown": "Nice to meet you,Chis.I learned a lot from you in default prediction competition.", "votes": null }, { "id": "1919614", "postDate": "08/30/2022 14:49:35", "content": "why can't we see the entire DNA and only a snapshot of it at a point in time?
\nIf I'm understanding your question, when we measure \"DNA\" we aren't actually measuring DNA but DNA accessibility. So while all the DNA is always there, there are various biological processes that are unwinding it and getting it ready for transcription. https://en.wikipedia.org/wiki/Epigenetics This is what the ATAC assay measures. DNA doesn't change over time, but accessibility does.
", "rawMarkdown": "*why can't we see the entire DNA and only a snapshot of it at a point in time?*\n\nIf I'm understanding your question, when we measure \"DNA\" we aren't actually measuring DNA but *DNA accessibility*. So while all the DNA is always there, there are various biological processes that are unwinding it and getting it ready for transcription. https://en.wikipedia.org/wiki/Epigenetics This is what the ATAC assay measures. DNA doesn't change over time, but accessibility does.", "votes": null }, { "id": "1920088", "postDate": "08/30/2022 21:59:26", "content": "Let us discuss \"Multiome\"
\nIt ls like that:
\nthere are GENES - which are EXACTLY THE SAME FOR ALL CELLS (- there are 20 000 of them - they are targets for Multiome)
\nbut each GENE is WORKING differently in each cell ! Let us not be precise on what is \"working\".
\nQuestion: Who controls each particular gene - how actively it is working in each particular cells ?
\nAnswer: ATAC-seq controls - features of Multiome (well, it is much much much more complicated and not known for modern science exactly, but still).
So: input - state of controler , and output - how actively genes are working.
", "rawMarkdown": "Let us discuss \"Multiome\"\n\nIt ls like that: \nthere are GENES - which are EXACTLY THE SAME FOR ALL CELLS (- there are 20 000 of them - they are targets for Multiome)\nbut each GENE is WORKING differently in each cell ! Let us not be precise on what is \"working\". \nQuestion: Who controls each particular gene - how actively it is working in each particular cells ? \nAnswer: ATAC-seq controls - features of Multiome (well, it is much much much more complicated and not known for modern science exactly, but still). \n\nSo: input - state of controler , and output - how actively genes are working.", "votes": null } ], "comments": [ { "id": 1918935, "author_name": "cdeotte", "author_url": "", "post_date": "08/30/2022 02:02:21", "content": "Here is a start
\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/346888
Nice to meet you,Chis.I learned a lot from you in default prediction competition.
", "votes": null, "replies": [] } ] }, { "id": 1919112, "author_name": "masato114", "author_url": "", "post_date": "08/30/2022 06:39:16", "content": "To my knowledge,
\naccording to this video gene expression is a combination of transcription (DNA -> mRNA) and translation (mRNA -> Protein) but in this context it seems to be equal to RNA?
\nYes, RNA is equal to messenger RNA (mRNA) in this context.
why can't we see the entire DNA and only a snapshot of it at a point in time?
\nI assume that is because the measurement process, which is composed of several steps like DNA/RNA extraction from cells and mixing with chemical reagent etc., is needed. So while this competition seems like a time-series competition, the time stamp is descrete.
what are the units in which we measure DNA/RNA/Proteins?
\nThe extracted DNA/RNA are fragmented and the nucleotides are sequenced, then each fragment is mapped onto the reference genome according the sequence, and then the fragments counted up in every gene region are finally recorded as the DNA/RNA count. Even regarding the protein measurment, since this competition utilizes the CITE-seq technology, each surface proteins are tagged with synthesized nucleotides and are measured in the same way as above. So the unit is none since the measurement is the number of fragments, I guess. This video might be helpful.
I am glad if you find this helpful.
", "votes": null, "replies": [] }, { "id": 1919614, "author_name": "lukeschiefelbein", "author_url": "", "post_date": "08/30/2022 14:49:35", "content": "why can't we see the entire DNA and only a snapshot of it at a point in time?
\nIf I'm understanding your question, when we measure \"DNA\" we aren't actually measuring DNA but DNA accessibility. So while all the DNA is always there, there are various biological processes that are unwinding it and getting it ready for transcription. https://en.wikipedia.org/wiki/Epigenetics This is what the ATAC assay measures. DNA doesn't change over time, but accessibility does.
", "votes": null, "replies": [] }, { "id": 1920088, "author_name": "alexandervc", "author_url": "", "post_date": "08/30/2022 21:59:26", "content": "Let us discuss \"Multiome\"
\nIt ls like that:
\nthere are GENES - which are EXACTLY THE SAME FOR ALL CELLS (- there are 20 000 of them - they are targets for Multiome)
\nbut each GENE is WORKING differently in each cell ! Let us not be precise on what is \"working\".
\nQuestion: Who controls each particular gene - how actively it is working in each particular cells ?
\nAnswer: ATAC-seq controls - features of Multiome (well, it is much much much more complicated and not known for modern science exactly, but still).
So: input - state of controler , and output - how actively genes are working.
", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "1918825": "This looks like a very exciting competition but I have trouble understanding the data and the task. Starting the thread that will hopefully lead me to be able to explain it to my 5yo daughter :) \n\n> Following the central dogma of molecular biology: DNA --> RNA-->Protein, your task is as follows:\n> For the Multiome samples: given chromatin accessibility, predict gene expression.\n> For the CITEseq samples: given gene expression, predict protein levels.\n\nLet's start with this one. My understanding it that there is a process going on in cells that starts with DNA, then creates RNA, and ultimately creates proteins. When we look at a specific cell at a specific point in time, I understand that we will see a snapshot of each of them (DNA/RNA/Protein) expressed in some units as a vector. The goal will be to predict one vector based on another vector. \n\n**Confused about**: \n- according to [this video](https://www.youtube.com/watch?v=whV_CkKT7F0) *gene expression* is a combination of transcription (DNA -> mRNA) and translation (mRNA -> Protein) but in this context it seems to be equal to *RNA*? \n- why can't we see the entire DNA and only a snapshot of it at a point in time? \n- what are the units in which we measure DNA/RNA/Proteins?\n\n*to be continued*", "1918935": "Here is a start\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/346888", "1919112": "To my knowledge,\n\n- *according to this video gene expression is a combination of transcription (DNA -> mRNA) and translation (mRNA -> Protein) but in this context it seems to be equal to RNA?*\nYes, RNA is equal to messenger RNA (mRNA) in this context.\n\n- *why can't we see the entire DNA and only a snapshot of it at a point in time?*\nI assume that is because the measurement process, which is composed of several steps like DNA/RNA extraction from cells and mixing with chemical reagent etc., is needed. So while this competition seems like a time-series competition, the time stamp is descrete.\n\n- *what are the units in which we measure DNA/RNA/Proteins?*\nThe extracted DNA/RNA are fragmented and the nucleotides are sequenced, then each fragment is mapped onto the reference genome according the sequence, and then the fragments counted up in every gene region are finally recorded as the DNA/RNA count. Even regarding the protein measurment, since this competition utilizes the CITE-seq technology, each surface proteins are tagged with synthesized nucleotides and are measured in the same way as above. So the unit is none since the measurement is the number of fragments, I guess. This [video](youtube.com/watch?v=hWWkpe4Ewgo) might be helpful.\n\nI am glad if you find this helpful.", "1919194": "Nice to meet you,Chis.I learned a lot from you in default prediction competition.", "1919614": "*why can't we see the entire DNA and only a snapshot of it at a point in time?*\n\nIf I'm understanding your question, when we measure \"DNA\" we aren't actually measuring DNA but *DNA accessibility*. So while all the DNA is always there, there are various biological processes that are unwinding it and getting it ready for transcription. https://en.wikipedia.org/wiki/Epigenetics This is what the ATAC assay measures. DNA doesn't change over time, but accessibility does.", "1920088": "Let us discuss \"Multiome\"\n\nIt ls like that: \nthere are GENES - which are EXACTLY THE SAME FOR ALL CELLS (- there are 20 000 of them - they are targets for Multiome)\nbut each GENE is WORKING differently in each cell ! Let us not be precise on what is \"working\". \nQuestion: Who controls each particular gene - how actively it is working in each particular cells ? \nAnswer: ATAC-seq controls - features of Multiome (well, it is much much much more complicated and not known for modern science exactly, but still). \n\nSo: input - state of controler , and output - how actively genes are working." }, "source": "meta" }