{ "id": 350314, "title": "Cell cycle analysis (it is mainly for research, not score improve)", "url": "/competitions/open-problems-multimodal/discussion/350314", "author_name": "", "post_date": "2022-09-05T07:39:40.702202800Z", "votes": 14, "comment_count": 5, "views": 0, "content": "

Introduction - to be written.
\nSee paper https://arxiv.org/abs/2208.05229 for some background.

\n

Some scripts e.g.:
\nMegakaryocytes:
\nhttps://www.kaggle.com/code/alexandervc/mmscel-cell-cycle-03-daybydaychage-megakaryocyt
\nAll cell types:
\nhttps://www.kaggle.com/alexandervc/mmscel-cell-cycle-03b-daybydaychange-allcelltypes

\n

It is a kind using Kaggle for taking personal notes, with some hope it might be useful for someone else, or it least for me to share with the colleagues.

\n

The words \"mobilized peripheral CD34+ \" - here \"MOBILIZED\" seems to mean that donors were given special drugs for weeks before the experiment such that their bone marrow cells move to the blood. It seems it is usually achieved by the proliferation stimulation. That is why we may expect stronger proliferation - so it might be different from other datasets with similar cells (typically there are datasets WITHOUT\" mobilization\").

\n

At day 3 many HSC cells are less proliferating:
\n\"\"

\n

At day 2 most HSC cells are ACTIVELY proliferating:
\n \"\"

\n

To get some flavor what these figures mean one may look at Figure 3 in the paper above.
\n(Or other papers).
\n\"\"

", "messages": [ { "id": "1926863", "postDate": "09/05/2022 07:39:40", "content": "

Introduction - to be written.
\nSee paper https://arxiv.org/abs/2208.05229 for some background.

\n

Some scripts e.g.:
\nMegakaryocytes:
\nhttps://www.kaggle.com/code/alexandervc/mmscel-cell-cycle-03-daybydaychage-megakaryocyt
\nAll cell types:
\nhttps://www.kaggle.com/alexandervc/mmscel-cell-cycle-03b-daybydaychange-allcelltypes

\n

It is a kind using Kaggle for taking personal notes, with some hope it might be useful for someone else, or it least for me to share with the colleagues.

\n

The words \"mobilized peripheral CD34+ \" - here \"MOBILIZED\" seems to mean that donors were given special drugs for weeks before the experiment such that their bone marrow cells move to the blood. It seems it is usually achieved by the proliferation stimulation. That is why we may expect stronger proliferation - so it might be different from other datasets with similar cells (typically there are datasets WITHOUT\" mobilization\").

\n

At day 3 many HSC cells are less proliferating:
\n\"\"

\n

At day 2 most HSC cells are ACTIVELY proliferating:
\n \"\"

\n

To get some flavor what these figures mean one may look at Figure 3 in the paper above.
\n(Or other papers).
\n\"\"

", "rawMarkdown": "Introduction - to be written. \nSee paper https://arxiv.org/abs/2208.05229 for some background.\n\nSome scripts e.g.: \nMegakaryocytes:\nhttps://www.kaggle.com/code/alexandervc/mmscel-cell-cycle-03-daybydaychage-megakaryocyt\nAll cell types: \nhttps://www.kaggle.com/alexandervc/mmscel-cell-cycle-03b-daybydaychange-allcelltypes\n\nIt is a kind using Kaggle for taking personal notes, with some hope it might be useful for someone else, or it least for me to share with the colleagues. \n\nThe words \"mobilized peripheral CD34+ \" - here \"MOBILIZED\" seems to mean that donors were given special drugs for weeks before the experiment such that their bone marrow cells move to the blood. It seems it is usually achieved by the proliferation stimulation. That is why we may expect stronger proliferation - so it might be different from other datasets with similar cells (typically there are datasets WITHOUT\" mobilization\").\n\nAt day 3 many HSC cells are less proliferating: \n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Faffe368b1d2a922d46fa7b73af1ee0b2%2FScreenshot%202022-09-05%20092420.png?generation=1662362689532478&alt=media)\n\nAt day 2 most HSC cells are ACTIVELY proliferating: \n ![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Fcaacddaba4a3ccb0ca92df443ebdd955%2FScreenshot%202022-09-05%20093113.png?generation=1662363339434887&alt=media)\n\nTo get some flavor what these figures mean one may look at Figure 3 in the paper above.\n(Or other papers).\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F69fcf93f86f635c775a6f65f4081e528%2FScreenshot%202022-09-05%20093632.png?generation=1662363508895265&alt=media)", "votes": null }, { "id": "1926964", "postDate": "09/05/2022 09:33:57", "content": "

Look on cell types present in the data. (The original picture - from Wikipedia https://en.wikipedia.org/wiki/Hematopoietic_stem_cell )
\nThe information may give us a rough idea which cell types are more close to each other.
\nWarning: it might be the Wikipedia information does not fully correspond to the data, because the data is about PROGENITORS, but the information about cell types themselves - need to clarify. May be look at the article organizers provided.

\n

There are only 869 cells which are marked B-cell Progenitors - it might be mistake of the cell type classification software.
\nIt is interesting to check. These cells are the only from the \"Lymphoid\" branch of the tree - all the others are from the \"Myeloid\".
\nQuestion to biologists: can B-cells progenitors be CD34+ ? Are B-cells indeed so rare in the blood, bone marrow, experiment like that ?

\n

\"\"

", "rawMarkdown": "Look on cell types present in the data. (The original picture - from Wikipedia https://en.wikipedia.org/wiki/Hematopoietic_stem_cell )\nThe information may give us a rough idea which cell types are more close to each other. \nWarning: it might be the Wikipedia information does not fully correspond to the data, because the data is about PROGENITORS, but the information about cell types themselves - need to clarify. May be look at the article organizers provided. \n\nThere are only 869 cells which are marked B-cell Progenitors - it might be mistake of the cell type classification software. \nIt is interesting to check. These cells are the only from the \"Lymphoid\" branch of the tree - all the others are from the \"Myeloid\".\nQuestion to biologists: can B-cells progenitors be CD34+ ? Are B-cells indeed so rare in the blood, bone marrow, experiment like that ? \n\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F1f9a32ac7d90f36b9268929c42e4ec3c%2FCellTypes.png?generation=1662370416820242&alt=media)", "votes": null }, { "id": "1927134", "postDate": "09/05/2022 12:07:35", "content": "

Very important and cool job!

\n

We are impressed and will share the useful site with you.
\nhttps://string-db.org/
\nThis site makes it easy to find out how genes are related to each other.

", "rawMarkdown": "Very important and cool job!\n\nWe are impressed and will share the useful site with you.\nhttps://string-db.org/\nThis site makes it easy to find out how genes are related to each other.", "votes": null }, { "id": "1927470", "postDate": "09/05/2022 16:33:04", "content": "

That's amazing, really appreciate your work. Thanks for sharing!

", "rawMarkdown": "That's amazing, really appreciate your work. Thanks for sharing!", "votes": null }, { "id": "1927525", "postDate": "09/05/2022 17:42:31", "content": "

The strange thing - it terms of proliferation day 3 looks more close to day 7 (test).
\nProliferation is higher for days 2,4 and lower for days 3 and 7.
\nIs it biology ?
\nThe crazy idea: one may even suspect that orgs named day 4 as day 3 and vice versa.

", "rawMarkdown": "The strange thing - it terms of proliferation day 3 looks more close to day 7 (test).\nProliferation is higher for days 2,4 and lower for days 3 and 7. \nIs it biology ? \nThe crazy idea: one may even suspect that orgs named day 4 as day 3 and vice versa.", "votes": null }, { "id": "1927599", "postDate": "09/05/2022 19:35:59", "content": "

Proliferation power decrease with a day for Multiome data:
\n\"\"

\n

For donors it is more or less homogeneous:
\n\"\"

\n

For comparison for CITE-seq data:
\n\"\"

\n

\"\"

\n

These plots are messy because all cell types are on one plot.
\nWhen we separate cell types - the \"cyclic\" structure becomes transparent - one can see the plots above.

", "rawMarkdown": "Proliferation power decrease with a day for Multiome data:\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F83ee9390faaee5a8c0e8f8550b9b1e00%2FScreenshot%202022-09-05%20213200.png?generation=1662406359106838&alt=media)\n\nFor donors it is more or less homogeneous:\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Fde9945eeaf2db102631e0ab798d4f72b%2FScreenshot%202022-09-05%20213449.png?generation=1662406527742473&alt=media)\n\nFor comparison for CITE-seq data: \n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F52d0c5d4a0efafb32392ac6cb04fef96%2FScreenshot%202022-09-05%20214030.png?generation=1662406884704036&alt=media)\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F05b6cd004aab97a0457558983ddb2299%2FScreenshot%202022-09-05%20214159.png?generation=1662406943701010&alt=media)\n\nThese plots are messy because all cell types are on one plot. \nWhen we separate cell types - the \"cyclic\" structure becomes transparent - one can see the plots above.", "votes": null } ], "comments": [ { "id": 1926964, "author_name": "alexandervc", "author_url": "", "post_date": "09/05/2022 09:33:57", "content": "

Look on cell types present in the data. (The original picture - from Wikipedia https://en.wikipedia.org/wiki/Hematopoietic_stem_cell )
\nThe information may give us a rough idea which cell types are more close to each other.
\nWarning: it might be the Wikipedia information does not fully correspond to the data, because the data is about PROGENITORS, but the information about cell types themselves - need to clarify. May be look at the article organizers provided.

\n

There are only 869 cells which are marked B-cell Progenitors - it might be mistake of the cell type classification software.
\nIt is interesting to check. These cells are the only from the \"Lymphoid\" branch of the tree - all the others are from the \"Myeloid\".
\nQuestion to biologists: can B-cells progenitors be CD34+ ? Are B-cells indeed so rare in the blood, bone marrow, experiment like that ?

\n

\"\"

", "votes": null, "replies": [] }, { "id": 1927134, "author_name": "miyawakiyoshifumi", "author_url": "", "post_date": "09/05/2022 12:07:35", "content": "

Very important and cool job!

\n

We are impressed and will share the useful site with you.
\nhttps://string-db.org/
\nThis site makes it easy to find out how genes are related to each other.

", "votes": null, "replies": [] }, { "id": 1927470, "author_name": "leandrodestefani", "author_url": "", "post_date": "09/05/2022 16:33:04", "content": "

That's amazing, really appreciate your work. Thanks for sharing!

", "votes": null, "replies": [] }, { "id": 1927525, "author_name": "alexandervc", "author_url": "", "post_date": "09/05/2022 17:42:31", "content": "

The strange thing - it terms of proliferation day 3 looks more close to day 7 (test).
\nProliferation is higher for days 2,4 and lower for days 3 and 7.
\nIs it biology ?
\nThe crazy idea: one may even suspect that orgs named day 4 as day 3 and vice versa.

", "votes": null, "replies": [] }, { "id": 1927599, "author_name": "alexandervc", "author_url": "", "post_date": "09/05/2022 19:35:59", "content": "

Proliferation power decrease with a day for Multiome data:
\n\"\"

\n

For donors it is more or less homogeneous:
\n\"\"

\n

For comparison for CITE-seq data:
\n\"\"

\n

\"\"

\n

These plots are messy because all cell types are on one plot.
\nWhen we separate cell types - the \"cyclic\" structure becomes transparent - one can see the plots above.

", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "1926863": "Introduction - to be written. \nSee paper https://arxiv.org/abs/2208.05229 for some background.\n\nSome scripts e.g.: \nMegakaryocytes:\nhttps://www.kaggle.com/code/alexandervc/mmscel-cell-cycle-03-daybydaychage-megakaryocyt\nAll cell types: \nhttps://www.kaggle.com/alexandervc/mmscel-cell-cycle-03b-daybydaychange-allcelltypes\n\nIt is a kind using Kaggle for taking personal notes, with some hope it might be useful for someone else, or it least for me to share with the colleagues. \n\nThe words \"mobilized peripheral CD34+ \" - here \"MOBILIZED\" seems to mean that donors were given special drugs for weeks before the experiment such that their bone marrow cells move to the blood. It seems it is usually achieved by the proliferation stimulation. That is why we may expect stronger proliferation - so it might be different from other datasets with similar cells (typically there are datasets WITHOUT\" mobilization\").\n\nAt day 3 many HSC cells are less proliferating: \n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Faffe368b1d2a922d46fa7b73af1ee0b2%2FScreenshot%202022-09-05%20092420.png?generation=1662362689532478&alt=media)\n\nAt day 2 most HSC cells are ACTIVELY proliferating: \n ![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Fcaacddaba4a3ccb0ca92df443ebdd955%2FScreenshot%202022-09-05%20093113.png?generation=1662363339434887&alt=media)\n\nTo get some flavor what these figures mean one may look at Figure 3 in the paper above.\n(Or other papers).\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F69fcf93f86f635c775a6f65f4081e528%2FScreenshot%202022-09-05%20093632.png?generation=1662363508895265&alt=media)", "1926964": "Look on cell types present in the data. (The original picture - from Wikipedia https://en.wikipedia.org/wiki/Hematopoietic_stem_cell )\nThe information may give us a rough idea which cell types are more close to each other. \nWarning: it might be the Wikipedia information does not fully correspond to the data, because the data is about PROGENITORS, but the information about cell types themselves - need to clarify. May be look at the article organizers provided. \n\nThere are only 869 cells which are marked B-cell Progenitors - it might be mistake of the cell type classification software. \nIt is interesting to check. These cells are the only from the \"Lymphoid\" branch of the tree - all the others are from the \"Myeloid\".\nQuestion to biologists: can B-cells progenitors be CD34+ ? Are B-cells indeed so rare in the blood, bone marrow, experiment like that ? \n\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F1f9a32ac7d90f36b9268929c42e4ec3c%2FCellTypes.png?generation=1662370416820242&alt=media)", "1927134": "Very important and cool job!\n\nWe are impressed and will share the useful site with you.\nhttps://string-db.org/\nThis site makes it easy to find out how genes are related to each other.", "1927470": "That's amazing, really appreciate your work. Thanks for sharing!", "1927525": "The strange thing - it terms of proliferation day 3 looks more close to day 7 (test).\nProliferation is higher for days 2,4 and lower for days 3 and 7. \nIs it biology ? \nThe crazy idea: one may even suspect that orgs named day 4 as day 3 and vice versa.", "1927599": "Proliferation power decrease with a day for Multiome data:\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F83ee9390faaee5a8c0e8f8550b9b1e00%2FScreenshot%202022-09-05%20213200.png?generation=1662406359106838&alt=media)\n\nFor donors it is more or less homogeneous:\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Fde9945eeaf2db102631e0ab798d4f72b%2FScreenshot%202022-09-05%20213449.png?generation=1662406527742473&alt=media)\n\nFor comparison for CITE-seq data: \n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F52d0c5d4a0efafb32392ac6cb04fef96%2FScreenshot%202022-09-05%20214030.png?generation=1662406884704036&alt=media)\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F05b6cd004aab97a0457558983ddb2299%2FScreenshot%202022-09-05%20214159.png?generation=1662406943701010&alt=media)\n\nThese plots are messy because all cell types are on one plot. \nWhen we separate cell types - the \"cyclic\" structure becomes transparent - one can see the plots above." }, "source": "meta" }