{ "id": 348117, "title": "A bit of domain knowledge", "url": "/competitions/open-problems-multimodal/discussion/348117", "author_name": "", "post_date": "2022-08-27T02:10:13.456281600Z", "votes": 13, "comment_count": 10, "views": 0, "content": "

I think it seems to be associated with Multiome (chromatin accessibility -> gene expression); however, there appears to be a significant barrier to CITEseq (gene expression -> protein).

", "messages": [ { "id": "1915467", "postDate": "08/27/2022 02:10:13", "content": "

I think it seems to be associated with Multiome (chromatin accessibility -> gene expression); however, there appears to be a significant barrier to CITEseq (gene expression -> protein).

", "rawMarkdown": "I think it seems to be associated with Multiome (chromatin accessibility -> gene expression); however, there appears to be a significant barrier to CITEseq (gene expression -> protein).", "votes": null }, { "id": "1917925", "postDate": "08/29/2022 06:55:11", "content": "

We can see seven cell types differentiate from Hematopoietic Stem Cells (HSC).
\n\"\"
\nhttps://en.wikipedia.org/wiki/Hematopoietic_stem_cell

\n

・Multime_targets (RNA expression)
\n\"\"

\n

・CITEseq_train (RNA expression)
\n\"\"

\n

・CITEseq_targets (Protein)
\n\"\"

\n

・CITEseq_test (RNA expression)
\n\"\"

", "rawMarkdown": "We can see seven cell types differentiate from Hematopoietic Stem Cells (HSC).\n![](https://user-images.githubusercontent.com/50528980/187141679-c56d0aee-a387-47d7-94e8-74fa620c2a21.png)\nhttps://en.wikipedia.org/wiki/Hematopoietic_stem_cell\n\n・Multime_targets (RNA expression)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F0355198a6d81ae2ec30aa41e71087f28%2F187071788-b73e4c8a-2fa6-42dc-95c7-f353957e3cd3.png?generation=1661755800759747&alt=media)\n\n\n・CITEseq_train (RNA expression)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F5769b41218c34abfb85582638c41d310%2F187076891-9e0982b3-9f3f-45db-9eeb-2e9d5bce8a21.png?generation=1661755954916783&alt=media)\n\n\n・CITEseq_targets (Protein)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F57f0102345fb9e04f9415d5d059a1be2%2F187071858-db366b93-e371-4368-a821-cb1bcf27bd58.png?generation=1661756003180414&alt=media)\n\n\n・CITEseq_test (RNA expression)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2Fac94352a40961ecdccdacf436ec16d33%2F187076838-6a1e59ea-382f-44bf-9cca-57753511c8e0.png?generation=1661756057480007&alt=media)", "votes": null }, { "id": "1918095", "postDate": "08/29/2022 10:11:33", "content": "

Nice !
\n・CITEseq_train (RNA expression) Day 3 is out of HSC are \"outliers\" - any idea why ? Low quality cells ? Have not checked MT-percent ?

\n

Here are similar plots from me: https://www.kaggle.com/code/alexandervc/mmscel-eda-bioinfo

", "rawMarkdown": "Nice ! \n・CITEseq_train (RNA expression) Day 3 is out of HSC are \"outliers\" - any idea why ? Low quality cells ? Have not checked MT-percent ? \n\nHere are similar plots from me: https://www.kaggle.com/code/alexandervc/mmscel-eda-bioinfo", "votes": null }, { "id": "1918126", "postDate": "08/29/2022 10:39:23", "content": "

Maybe so! I did not check for ribosomal or mitochondrial genes because I thought quality control was already in place since they were normalized.

\n

But it looks like CITEseq_test (RNA expression) has a similar Day 3's of HSC.\"\"

", "rawMarkdown": "Maybe so! I did not check for ribosomal or mitochondrial genes because I thought quality control was already in place since they were normalized.\n\nBut it looks like CITEseq_test (RNA expression) has a similar Day 3's of HSC.![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F897687c2f4873091375ecafc1a5bd6e3%2F187076838-6a1e59ea-382f-44bf-9cca-57753511c8e0.png?generation=1661769562023629&alt=media)", "votes": null }, { "id": "1918134", "postDate": "08/29/2022 10:47:27", "content": "

Day 3's of HSC may be the beginning of some changes.

", "rawMarkdown": "Day 3's of HSC may be the beginning of some changes.", "votes": null }, { "id": "1918248", "postDate": "08/29/2022 12:25:36", "content": "

As expected, the CITEseq_train (RNA expression) data is of high quality, with little mitochondrial RNA.
\n\"\"

", "rawMarkdown": "As expected, the CITEseq_train (RNA expression) data is of high quality, with little mitochondrial RNA.\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F9a43bd98ed352c89fac7b45a4b0f7989%2FScreen%20Shot%202022-08-29%20at%2021.23.10.png?generation=1661775954631374&alt=media)", "votes": null }, { "id": "1918251", "postDate": "08/29/2022 12:32:21", "content": "

Stem cells can differentiate upon stimulation. It may be that Day 3's of HSCs are trying to differentiate into some kind of mesenchymal-like cell.

\n

\"\"

\n

\"\"

", "rawMarkdown": "Stem cells can differentiate upon stimulation. It may be that Day 3's of HSCs are trying to differentiate into some kind of mesenchymal-like cell.\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F51c490d110f0a7ca1b03b70b8f314613%2FScreen%20Shot%202022-08-29%20at%2021.26.34.png?generation=1661776328023207&alt=media)\n\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F3de67c2100997140deee5d3405d55b1f%2FScreen%20Shot%202022-08-29%20at%2021.27.03.png?generation=1661776339460684&alt=media)", "votes": null }, { "id": "1919034", "postDate": "08/30/2022 04:37:09", "content": "

That cells seems to be in G0.
\nIt is strange the next day , G0 decrease.
\nPS
\nI will open notebook a bit later

\n

\"\"

", "rawMarkdown": "That cells seems to be in G0.\nIt is strange the next day , G0 decrease.\nPS\nI will open notebook a bit later\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Fa30d738cccac6cfa55251cc1d8b89ee6%2FIMG_20220830_063341_588.jpg?generation=1661834091952436&alt=media)", "votes": null }, { "id": "1919087", "postDate": "08/30/2022 06:00:45", "content": "

By the way, can you share the notebook please

", "rawMarkdown": "By the way, can you share the notebook please", "votes": null }, { "id": "1919096", "postDate": "08/30/2022 06:12:03", "content": "

Okay! Please give me some time! I will organize codes and share the codes and datasets.

", "rawMarkdown": "Okay! Please give me some time! I will organize codes and share the codes and datasets.", "votes": null }, { "id": "1920546", "postDate": "08/31/2022 07:55:44", "content": "

By the way we organizing educational/research webinars around that competition.
\nWould you be so kind to make a talk (even a short) ? May be giving some story around - single cell analysis, scanpy , so on …

\n

See:
\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348661
\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348293

", "rawMarkdown": "By the way we organizing educational/research webinars around that competition. \nWould you be so kind to make a talk (even a short) ? May be giving some story around - single cell analysis, scanpy , so on ... \n\nSee: \nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348661\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348293", "votes": null } ], "comments": [ { "id": 1917925, "author_name": "kfurudate", "author_url": "", "post_date": "08/29/2022 06:55:11", "content": "

We can see seven cell types differentiate from Hematopoietic Stem Cells (HSC).
\n\"\"
\nhttps://en.wikipedia.org/wiki/Hematopoietic_stem_cell

\n

・Multime_targets (RNA expression)
\n\"\"

\n

・CITEseq_train (RNA expression)
\n\"\"

\n

・CITEseq_targets (Protein)
\n\"\"

\n

・CITEseq_test (RNA expression)
\n\"\"

", "votes": null, "replies": [ { "id": 1918095, "author_name": "alexandervc", "author_url": "", "post_date": "08/29/2022 10:11:33", "content": "

Nice !
\n・CITEseq_train (RNA expression) Day 3 is out of HSC are \"outliers\" - any idea why ? Low quality cells ? Have not checked MT-percent ?

\n

Here are similar plots from me: https://www.kaggle.com/code/alexandervc/mmscel-eda-bioinfo

", "votes": null, "replies": [] }, { "id": 1918126, "author_name": "kfurudate", "author_url": "", "post_date": "08/29/2022 10:39:23", "content": "

Maybe so! I did not check for ribosomal or mitochondrial genes because I thought quality control was already in place since they were normalized.

\n

But it looks like CITEseq_test (RNA expression) has a similar Day 3's of HSC.\"\"

", "votes": null, "replies": [] }, { "id": 1918134, "author_name": "kfurudate", "author_url": "", "post_date": "08/29/2022 10:47:27", "content": "

Day 3's of HSC may be the beginning of some changes.

", "votes": null, "replies": [] }, { "id": 1918248, "author_name": "kfurudate", "author_url": "", "post_date": "08/29/2022 12:25:36", "content": "

As expected, the CITEseq_train (RNA expression) data is of high quality, with little mitochondrial RNA.
\n\"\"

", "votes": null, "replies": [] }, { "id": 1918251, "author_name": "kfurudate", "author_url": "", "post_date": "08/29/2022 12:32:21", "content": "

Stem cells can differentiate upon stimulation. It may be that Day 3's of HSCs are trying to differentiate into some kind of mesenchymal-like cell.

\n

\"\"

\n

\"\"

", "votes": null, "replies": [] }, { "id": 1919034, "author_name": "alexandervc", "author_url": "", "post_date": "08/30/2022 04:37:09", "content": "

That cells seems to be in G0.
\nIt is strange the next day , G0 decrease.
\nPS
\nI will open notebook a bit later

\n

\"\"

", "votes": null, "replies": [] } ] }, { "id": 1919087, "author_name": "alexandervc", "author_url": "", "post_date": "08/30/2022 06:00:45", "content": "

By the way, can you share the notebook please

", "votes": null, "replies": [ { "id": 1919096, "author_name": "kfurudate", "author_url": "", "post_date": "08/30/2022 06:12:03", "content": "

Okay! Please give me some time! I will organize codes and share the codes and datasets.

", "votes": null, "replies": [] }, { "id": 1920546, "author_name": "alexandervc", "author_url": "", "post_date": "08/31/2022 07:55:44", "content": "

By the way we organizing educational/research webinars around that competition.
\nWould you be so kind to make a talk (even a short) ? May be giving some story around - single cell analysis, scanpy , so on …

\n

See:
\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348661
\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348293

", "votes": null, "replies": [] } ] } ], "raw_markdown_by_id": { "1915467": "I think it seems to be associated with Multiome (chromatin accessibility -> gene expression); however, there appears to be a significant barrier to CITEseq (gene expression -> protein).", "1917925": "We can see seven cell types differentiate from Hematopoietic Stem Cells (HSC).\n![](https://user-images.githubusercontent.com/50528980/187141679-c56d0aee-a387-47d7-94e8-74fa620c2a21.png)\nhttps://en.wikipedia.org/wiki/Hematopoietic_stem_cell\n\n・Multime_targets (RNA expression)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F0355198a6d81ae2ec30aa41e71087f28%2F187071788-b73e4c8a-2fa6-42dc-95c7-f353957e3cd3.png?generation=1661755800759747&alt=media)\n\n\n・CITEseq_train (RNA expression)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F5769b41218c34abfb85582638c41d310%2F187076891-9e0982b3-9f3f-45db-9eeb-2e9d5bce8a21.png?generation=1661755954916783&alt=media)\n\n\n・CITEseq_targets (Protein)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F57f0102345fb9e04f9415d5d059a1be2%2F187071858-db366b93-e371-4368-a821-cb1bcf27bd58.png?generation=1661756003180414&alt=media)\n\n\n・CITEseq_test (RNA expression)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2Fac94352a40961ecdccdacf436ec16d33%2F187076838-6a1e59ea-382f-44bf-9cca-57753511c8e0.png?generation=1661756057480007&alt=media)", "1918095": "Nice ! \n・CITEseq_train (RNA expression) Day 3 is out of HSC are \"outliers\" - any idea why ? Low quality cells ? Have not checked MT-percent ? \n\nHere are similar plots from me: https://www.kaggle.com/code/alexandervc/mmscel-eda-bioinfo", "1918126": "Maybe so! I did not check for ribosomal or mitochondrial genes because I thought quality control was already in place since they were normalized.\n\nBut it looks like CITEseq_test (RNA expression) has a similar Day 3's of HSC.![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F897687c2f4873091375ecafc1a5bd6e3%2F187076838-6a1e59ea-382f-44bf-9cca-57753511c8e0.png?generation=1661769562023629&alt=media)", "1918134": "Day 3's of HSC may be the beginning of some changes.", "1918248": "As expected, the CITEseq_train (RNA expression) data is of high quality, with little mitochondrial RNA.\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F9a43bd98ed352c89fac7b45a4b0f7989%2FScreen%20Shot%202022-08-29%20at%2021.23.10.png?generation=1661775954631374&alt=media)", "1918251": "Stem cells can differentiate upon stimulation. It may be that Day 3's of HSCs are trying to differentiate into some kind of mesenchymal-like cell.\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F51c490d110f0a7ca1b03b70b8f314613%2FScreen%20Shot%202022-08-29%20at%2021.26.34.png?generation=1661776328023207&alt=media)\n\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F3284781%2F3de67c2100997140deee5d3405d55b1f%2FScreen%20Shot%202022-08-29%20at%2021.27.03.png?generation=1661776339460684&alt=media)", "1919034": "That cells seems to be in G0.\nIt is strange the next day , G0 decrease.\nPS\nI will open notebook a bit later\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Fa30d738cccac6cfa55251cc1d8b89ee6%2FIMG_20220830_063341_588.jpg?generation=1661834091952436&alt=media)", "1919087": "By the way, can you share the notebook please", "1919096": "Okay! Please give me some time! I will organize codes and share the codes and datasets.", "1920546": "By the way we organizing educational/research webinars around that competition. \nWould you be so kind to make a talk (even a short) ? May be giving some story around - single cell analysis, scanpy , so on ... \n\nSee: \nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348661\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348293" }, "source": "meta" }