{
  "id": 463546,
  "title": "Detailed Analysis of Gene Cluster Stability",
  "url": "/competitions/open-problems-single-cell-perturbations/discussion/463546",
  "author_name": "",
  "post_date": "2023-12-25T20:51:43.193098400Z",
  "votes": 8,
  "comment_count": 1,
  "views": 0,
  "content": "<p><strong>Detailed Analysis of Gene Cluster Stability</strong></p>\n<p>Motivated by the insightful analysis found in the <a href=\"https://www.kaggle.com/competitions/open-problems-single-cell-perturbations/discussion/461159\" target=\"_blank\">Kaggle Discussion</a>, which highlighted that housekeeping genes are less prone to variations compared to other gene types, this study delves into the differential stability of gene clusters when subjected to various conditions. We focus on genes that exhibit expression levels surpassing those of housekeeping genes, potentially signaling a higher degree of alteration in response to stressors. Below is a detailed categorization of these gene groups by their sources:</p>\n<h3>Groups Without Effects Above the Baseline:</h3>\n<p>These groups did not show significant deviations from the expected baseline stability.</p>\n<p><strong>From Wikipedia (Housekeeping gene)</strong>: <a href=\"https://en.wikipedia.org/wiki/Housekeeping_gene\" target=\"_blank\">Housekeeping gene - Wikipedia</a></p>\n<ul>\n<li>Transcription Factors</li>\n<li>RNA Splicing Factors</li>\n<li>Translation Factors</li>\n<li>TRNA Synthesis Genes</li>\n<li>Ribosomal Proteins</li>\n<li>Mitochondrial Ribosomal Proteins</li>\n<li>NADH Dehydrogenase Enzymes</li>\n<li>Cytochrome C Oxidase Enzymes</li>\n</ul>\n<p><strong>From Kaggle Notebook (Analysis by Alexander Chervov)</strong>: <a href=\"https://www.kaggle.com/code/alexandervc/op2-eda-baseline-s?scriptVersionId=147818286&amp;cellId=32\" target=\"_blank\">Kaggle Notebook - Cell Proliferation Cycle Genes</a></p>\n<ul>\n<li>Cell Proliferation Cycle Genes<ul>\n<li>Tirosh: A refined and reliable list.</li>\n<li>Freeman: A more extensive list with diverse functionalities.</li></ul></li>\n</ul>\n<p><strong>From Gene Ontology</strong>: <a href=\"https://www.informatics.jax.org/vocab/gene_ontology/GO:0033554\" target=\"_blank\">Gene Ontology</a></p>\n<ul>\n<li>Cellular Response to Stress</li>\n</ul>\n<p><strong>From GSEA-MSigDB</strong>: <a href=\"https://www.gsea-msigdb.org\" target=\"_blank\">GSEA-MSigDB</a></p>\n<ul>\n<li>BIOCARTA_HSP27_PATHWAY</li>\n<li>GOBP_CELLULAR_RESPONSE_TO_HEAT</li>\n<li>HALLMARK_UV_RESPONSE_UP</li>\n<li>PID_HIF1A_PATHWAY</li>\n<li>GOMF_HEAT_SHOCK_PROTEIN_BINDING</li>\n<li>HALLMARK_COMPLEMENT</li>\n<li>HALLMARK_APOPTOSIS</li>\n<li>HALLMARK_APICAL_JUNCTION</li>\n<li>HALLMARK_ESTROGEN_RESPONSE_LATE</li>\n<li>HALLMARK_TNFA_SIGNALING_VIA_NFKB</li>\n<li>HALLMARK_KRAS_SIGNALING_UP</li>\n<li>HALLMARK_COAGULATION</li>\n<li>BIOCARTA_EIF_PATHWAY</li>\n</ul>\n<p><strong>From Kaggle Notebook (Plant Homology Research)</strong>: <a href=\"https://www.kaggle.com/nikolenkosergei/gene-homology-search\" target=\"_blank\">Kaggle Notebook - Plant Homology Research</a></p>\n<ul>\n<li>Plant Homo</li>\n</ul>\n<h3>Groups With Effects Above the Baseline:</h3>\n<p>These gene groups exhibit a level of stability that suggests an adaptive dynamic response to environmental stress.</p>\n<p><strong>From GSEA-MSigDB</strong> (Referencing Los Rodriguez [Saez Lab] writeup): <a href=\"https://www.gsea-msigdb.org\" target=\"_blank\">GSEA-MSigDB</a>, <a href=\"https://www.kaggle.com/competitions/open-problems-single-cell-perturbations/discussion/461225\" target=\"_blank\">6th Place Solution Writeup</a></p>\n<ul>\n<li>HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION<br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F7b7e01384f681d7ed2624c8449810096%2F3.jpeg?generation=1703537496099980&amp;alt=media\" alt=\"\"></li>\n<li>HALLMARK_HYPOXIA<br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F5fba7ce0faf2eeaaaa83e62a64a31d34%2F1.png?generation=1703537469280388&amp;alt=media\" alt=\"\"></li>\n<li>BIOCARTA_HIF_PATHWAY<br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F83e41cd551d976c889154bf087b078ce%2F2.jpeg?generation=1703537481720642&amp;alt=media\" alt=\"\"></li>\n</ul>\n<p>These observations prompt further investigation into the biological mechanisms and underscore the need for careful consideration of potential data or analytical artifacts. The increased sensitivity of certain gene groups to external conditions warrants a closer look to fully understand their implications.</p>\n<p><a href=\"https://www.kaggle.com/code/nikolenkosergei/op2-eda-housekeeping-genes\" target=\"_blank\"><strong>View My Notebook</strong></a></p>\n<hr>\n<p><em>Note: \"Effects above the baseline\" refers to gene expressions exceeding the stability or deviations typically expected for housekeeping genes.</em></p>",
  "messages": [
    {
      "id": "2574354",
      "postDate": "12/25/2023 20:51:43",
      "content": "<p><strong>Detailed Analysis of Gene Cluster Stability</strong></p>\n<p>Motivated by the insightful analysis found in the <a href=\"https://www.kaggle.com/competitions/open-problems-single-cell-perturbations/discussion/461159\" target=\"_blank\">Kaggle Discussion</a>, which highlighted that housekeeping genes are less prone to variations compared to other gene types, this study delves into the differential stability of gene clusters when subjected to various conditions. We focus on genes that exhibit expression levels surpassing those of housekeeping genes, potentially signaling a higher degree of alteration in response to stressors. Below is a detailed categorization of these gene groups by their sources:</p>\n<h3>Groups Without Effects Above the Baseline:</h3>\n<p>These groups did not show significant deviations from the expected baseline stability.</p>\n<p><strong>From Wikipedia (Housekeeping gene)</strong>: <a href=\"https://en.wikipedia.org/wiki/Housekeeping_gene\" target=\"_blank\">Housekeeping gene - Wikipedia</a></p>\n<ul>\n<li>Transcription Factors</li>\n<li>RNA Splicing Factors</li>\n<li>Translation Factors</li>\n<li>TRNA Synthesis Genes</li>\n<li>Ribosomal Proteins</li>\n<li>Mitochondrial Ribosomal Proteins</li>\n<li>NADH Dehydrogenase Enzymes</li>\n<li>Cytochrome C Oxidase Enzymes</li>\n</ul>\n<p><strong>From Kaggle Notebook (Analysis by Alexander Chervov)</strong>: <a href=\"https://www.kaggle.com/code/alexandervc/op2-eda-baseline-s?scriptVersionId=147818286&amp;cellId=32\" target=\"_blank\">Kaggle Notebook - Cell Proliferation Cycle Genes</a></p>\n<ul>\n<li>Cell Proliferation Cycle Genes<ul>\n<li>Tirosh: A refined and reliable list.</li>\n<li>Freeman: A more extensive list with diverse functionalities.</li></ul></li>\n</ul>\n<p><strong>From Gene Ontology</strong>: <a href=\"https://www.informatics.jax.org/vocab/gene_ontology/GO:0033554\" target=\"_blank\">Gene Ontology</a></p>\n<ul>\n<li>Cellular Response to Stress</li>\n</ul>\n<p><strong>From GSEA-MSigDB</strong>: <a href=\"https://www.gsea-msigdb.org\" target=\"_blank\">GSEA-MSigDB</a></p>\n<ul>\n<li>BIOCARTA_HSP27_PATHWAY</li>\n<li>GOBP_CELLULAR_RESPONSE_TO_HEAT</li>\n<li>HALLMARK_UV_RESPONSE_UP</li>\n<li>PID_HIF1A_PATHWAY</li>\n<li>GOMF_HEAT_SHOCK_PROTEIN_BINDING</li>\n<li>HALLMARK_COMPLEMENT</li>\n<li>HALLMARK_APOPTOSIS</li>\n<li>HALLMARK_APICAL_JUNCTION</li>\n<li>HALLMARK_ESTROGEN_RESPONSE_LATE</li>\n<li>HALLMARK_TNFA_SIGNALING_VIA_NFKB</li>\n<li>HALLMARK_KRAS_SIGNALING_UP</li>\n<li>HALLMARK_COAGULATION</li>\n<li>BIOCARTA_EIF_PATHWAY</li>\n</ul>\n<p><strong>From Kaggle Notebook (Plant Homology Research)</strong>: <a href=\"https://www.kaggle.com/nikolenkosergei/gene-homology-search\" target=\"_blank\">Kaggle Notebook - Plant Homology Research</a></p>\n<ul>\n<li>Plant Homo</li>\n</ul>\n<h3>Groups With Effects Above the Baseline:</h3>\n<p>These gene groups exhibit a level of stability that suggests an adaptive dynamic response to environmental stress.</p>\n<p><strong>From GSEA-MSigDB</strong> (Referencing Los Rodriguez [Saez Lab] writeup): <a href=\"https://www.gsea-msigdb.org\" target=\"_blank\">GSEA-MSigDB</a>, <a href=\"https://www.kaggle.com/competitions/open-problems-single-cell-perturbations/discussion/461225\" target=\"_blank\">6th Place Solution Writeup</a></p>\n<ul>\n<li>HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION<br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F7b7e01384f681d7ed2624c8449810096%2F3.jpeg?generation=1703537496099980&amp;alt=media\" alt=\"\"></li>\n<li>HALLMARK_HYPOXIA<br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F5fba7ce0faf2eeaaaa83e62a64a31d34%2F1.png?generation=1703537469280388&amp;alt=media\" alt=\"\"></li>\n<li>BIOCARTA_HIF_PATHWAY<br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F83e41cd551d976c889154bf087b078ce%2F2.jpeg?generation=1703537481720642&amp;alt=media\" alt=\"\"></li>\n</ul>\n<p>These observations prompt further investigation into the biological mechanisms and underscore the need for careful consideration of potential data or analytical artifacts. The increased sensitivity of certain gene groups to external conditions warrants a closer look to fully understand their implications.</p>\n<p><a href=\"https://www.kaggle.com/code/nikolenkosergei/op2-eda-housekeeping-genes\" target=\"_blank\"><strong>View My Notebook</strong></a></p>\n<hr>\n<p><em>Note: \"Effects above the baseline\" refers to gene expressions exceeding the stability or deviations typically expected for housekeeping genes.</em></p>",
      "rawMarkdown": "**Detailed Analysis of Gene Cluster Stability**\n\nMotivated by the insightful analysis found in the [Kaggle Discussion](https://www.kaggle.com/competitions/open-problems-single-cell-perturbations/discussion/461159), which highlighted that housekeeping genes are less prone to variations compared to other gene types, this study delves into the differential stability of gene clusters when subjected to various conditions. We focus on genes that exhibit expression levels surpassing those of housekeeping genes, potentially signaling a higher degree of alteration in response to stressors. Below is a detailed categorization of these gene groups by their sources:\n\n### Groups Without Effects Above the Baseline:\nThese groups did not show significant deviations from the expected baseline stability.\n\n**From Wikipedia (Housekeeping gene)**: [Housekeeping gene - Wikipedia](https://en.wikipedia.org/wiki/Housekeeping_gene)\n- Transcription Factors\n- RNA Splicing Factors\n- Translation Factors\n- TRNA Synthesis Genes\n- Ribosomal Proteins\n- Mitochondrial Ribosomal Proteins\n- NADH Dehydrogenase Enzymes\n- Cytochrome C Oxidase Enzymes\n\n**From Kaggle Notebook (Analysis by Alexander Chervov)**: [Kaggle Notebook - Cell Proliferation Cycle Genes](https://www.kaggle.com/code/alexandervc/op2-eda-baseline-s?scriptVersionId=147818286&cellId=32)\n- Cell Proliferation Cycle Genes\n  - Tirosh: A refined and reliable list.\n  - Freeman: A more extensive list with diverse functionalities.\n\n**From Gene Ontology**: [Gene Ontology](https://www.informatics.jax.org/vocab/gene_ontology/GO:0033554)\n- Cellular Response to Stress\n\n**From GSEA-MSigDB**: [GSEA-MSigDB](https://www.gsea-msigdb.org)\n- BIOCARTA_HSP27_PATHWAY\n- GOBP_CELLULAR_RESPONSE_TO_HEAT\n- HALLMARK_UV_RESPONSE_UP\n- PID_HIF1A_PATHWAY\n- GOMF_HEAT_SHOCK_PROTEIN_BINDING\n- HALLMARK_COMPLEMENT\n- HALLMARK_APOPTOSIS\n- HALLMARK_APICAL_JUNCTION\n- HALLMARK_ESTROGEN_RESPONSE_LATE\n- HALLMARK_TNFA_SIGNALING_VIA_NFKB\n- HALLMARK_KRAS_SIGNALING_UP\n- HALLMARK_COAGULATION\n- BIOCARTA_EIF_PATHWAY\n\n**From Kaggle Notebook (Plant Homology Research)**: [Kaggle Notebook - Plant Homology Research](https://www.kaggle.com/nikolenkosergei/gene-homology-search)\n- Plant Homo\n\n### Groups With Effects Above the Baseline:\nThese gene groups exhibit a level of stability that suggests an adaptive dynamic response to environmental stress.\n\n**From GSEA-MSigDB** (Referencing Los Rodriguez [Saez Lab] writeup): [GSEA-MSigDB](https://www.gsea-msigdb.org), [6th Place Solution Writeup](https://www.kaggle.com/competitions/open-problems-single-cell-perturbations/discussion/461225)\n\n- HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F7b7e01384f681d7ed2624c8449810096%2F3.jpeg?generation=1703537496099980&alt=media)\n- HALLMARK_HYPOXIA\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F5fba7ce0faf2eeaaaa83e62a64a31d34%2F1.png?generation=1703537469280388&alt=media)\n- BIOCARTA_HIF_PATHWAY\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F83e41cd551d976c889154bf087b078ce%2F2.jpeg?generation=1703537481720642&alt=media)\n\nThese observations prompt further investigation into the biological mechanisms and underscore the need for careful consideration of potential data or analytical artifacts. The increased sensitivity of certain gene groups to external conditions warrants a closer look to fully understand their implications.\n\n[**View My Notebook**](https://www.kaggle.com/code/nikolenkosergei/op2-eda-housekeeping-genes)\n\n---\n\n*Note: \"Effects above the baseline\" refers to gene expressions exceeding the stability or deviations typically expected for housekeeping genes.*",
      "votes": null
    },
    {
      "id": "2576420",
      "postDate": "12/27/2023 18:15:37",
      "content": "<p>cI have checked a few other families of genes that are related to stress response. <br>\n1) Sirtuins, they take part in maintaining normal chromatin condensation state, in DNA damage response and repair, modulate oxidative stress and energy metabolism<br>\n2) Genes associated with sirtuins - graph shows only genes related to regulation of metabolism<br>\n3) Autophagy genes, usually elevated during stress as cell clears damaged proteins and organelles, and maintains metabolic balance</p>\n<p>Here is graph for 1)<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2Fe5b5494ec2f9c8c748042039004e976c%2FScreenshot%202023-12-29%20at%2020.55.17.png?generation=1703854579788691&amp;alt=media\" alt=\"\"><br>\nHere is for 2)<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2F633a0adea171d6b56a18c4eca2fae656%2FScreenshot%202023-12-26%20at%2000.31.47.png?generation=1703700722597563&amp;alt=media\" alt=\"\"><br>\nAnd here is for 3)<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2F601aa4c57aef71f02dc6d05c8d830352%2Fautophagy.png?generation=1703700752516429&amp;alt=media\" alt=\"\"></p>\n<p>For these group it does not seem that the expression is elevated. Interestingly that expression of 7 sirtuins is on the level with housekeeping genes.</p>\n<p>link to notebook: <a href=\"https://www.kaggle.com/code/sankkan/op2-eda-housekeeping-genes-sirtuins-autophagy/edit/run/156987950\" target=\"_blank\">https://www.kaggle.com/code/sankkan/op2-eda-housekeeping-genes-sirtuins-autophagy/edit/run/156987950</a></p>",
      "rawMarkdown": "cI have checked a few other families of genes that are related to stress response. \n1) Sirtuins, they take part in maintaining normal chromatin condensation state, in DNA damage response and repair, modulate oxidative stress and energy metabolism\n2) Genes associated with sirtuins - graph shows only genes related to regulation of metabolism\n3) Autophagy genes, usually elevated during stress as cell clears damaged proteins and organelles, and maintains metabolic balance\n\nHere is graph for 1)![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2Fe5b5494ec2f9c8c748042039004e976c%2FScreenshot%202023-12-29%20at%2020.55.17.png?generation=1703854579788691&alt=media)\nHere is for 2)![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2F633a0adea171d6b56a18c4eca2fae656%2FScreenshot%202023-12-26%20at%2000.31.47.png?generation=1703700722597563&alt=media)\nAnd here is for 3)![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2F601aa4c57aef71f02dc6d05c8d830352%2Fautophagy.png?generation=1703700752516429&alt=media)\n\nFor these group it does not seem that the expression is elevated. Interestingly that expression of 7 sirtuins is on the level with housekeeping genes.\n\nlink to notebook: https://www.kaggle.com/code/sankkan/op2-eda-housekeeping-genes-sirtuins-autophagy/edit/run/156987950",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 2576420,
      "author_name": "sankkan",
      "author_url": "",
      "post_date": "12/27/2023 18:15:37",
      "content": "<p>cI have checked a few other families of genes that are related to stress response. <br>\n1) Sirtuins, they take part in maintaining normal chromatin condensation state, in DNA damage response and repair, modulate oxidative stress and energy metabolism<br>\n2) Genes associated with sirtuins - graph shows only genes related to regulation of metabolism<br>\n3) Autophagy genes, usually elevated during stress as cell clears damaged proteins and organelles, and maintains metabolic balance</p>\n<p>Here is graph for 1)<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2Fe5b5494ec2f9c8c748042039004e976c%2FScreenshot%202023-12-29%20at%2020.55.17.png?generation=1703854579788691&amp;alt=media\" alt=\"\"><br>\nHere is for 2)<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2F633a0adea171d6b56a18c4eca2fae656%2FScreenshot%202023-12-26%20at%2000.31.47.png?generation=1703700722597563&amp;alt=media\" alt=\"\"><br>\nAnd here is for 3)<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2F601aa4c57aef71f02dc6d05c8d830352%2Fautophagy.png?generation=1703700752516429&amp;alt=media\" alt=\"\"></p>\n<p>For these group it does not seem that the expression is elevated. Interestingly that expression of 7 sirtuins is on the level with housekeeping genes.</p>\n<p>link to notebook: <a href=\"https://www.kaggle.com/code/sankkan/op2-eda-housekeeping-genes-sirtuins-autophagy/edit/run/156987950\" target=\"_blank\">https://www.kaggle.com/code/sankkan/op2-eda-housekeeping-genes-sirtuins-autophagy/edit/run/156987950</a></p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "2574354": "**Detailed Analysis of Gene Cluster Stability**\n\nMotivated by the insightful analysis found in the [Kaggle Discussion](https://www.kaggle.com/competitions/open-problems-single-cell-perturbations/discussion/461159), which highlighted that housekeeping genes are less prone to variations compared to other gene types, this study delves into the differential stability of gene clusters when subjected to various conditions. We focus on genes that exhibit expression levels surpassing those of housekeeping genes, potentially signaling a higher degree of alteration in response to stressors. Below is a detailed categorization of these gene groups by their sources:\n\n### Groups Without Effects Above the Baseline:\nThese groups did not show significant deviations from the expected baseline stability.\n\n**From Wikipedia (Housekeeping gene)**: [Housekeeping gene - Wikipedia](https://en.wikipedia.org/wiki/Housekeeping_gene)\n- Transcription Factors\n- RNA Splicing Factors\n- Translation Factors\n- TRNA Synthesis Genes\n- Ribosomal Proteins\n- Mitochondrial Ribosomal Proteins\n- NADH Dehydrogenase Enzymes\n- Cytochrome C Oxidase Enzymes\n\n**From Kaggle Notebook (Analysis by Alexander Chervov)**: [Kaggle Notebook - Cell Proliferation Cycle Genes](https://www.kaggle.com/code/alexandervc/op2-eda-baseline-s?scriptVersionId=147818286&cellId=32)\n- Cell Proliferation Cycle Genes\n  - Tirosh: A refined and reliable list.\n  - Freeman: A more extensive list with diverse functionalities.\n\n**From Gene Ontology**: [Gene Ontology](https://www.informatics.jax.org/vocab/gene_ontology/GO:0033554)\n- Cellular Response to Stress\n\n**From GSEA-MSigDB**: [GSEA-MSigDB](https://www.gsea-msigdb.org)\n- BIOCARTA_HSP27_PATHWAY\n- GOBP_CELLULAR_RESPONSE_TO_HEAT\n- HALLMARK_UV_RESPONSE_UP\n- PID_HIF1A_PATHWAY\n- GOMF_HEAT_SHOCK_PROTEIN_BINDING\n- HALLMARK_COMPLEMENT\n- HALLMARK_APOPTOSIS\n- HALLMARK_APICAL_JUNCTION\n- HALLMARK_ESTROGEN_RESPONSE_LATE\n- HALLMARK_TNFA_SIGNALING_VIA_NFKB\n- HALLMARK_KRAS_SIGNALING_UP\n- HALLMARK_COAGULATION\n- BIOCARTA_EIF_PATHWAY\n\n**From Kaggle Notebook (Plant Homology Research)**: [Kaggle Notebook - Plant Homology Research](https://www.kaggle.com/nikolenkosergei/gene-homology-search)\n- Plant Homo\n\n### Groups With Effects Above the Baseline:\nThese gene groups exhibit a level of stability that suggests an adaptive dynamic response to environmental stress.\n\n**From GSEA-MSigDB** (Referencing Los Rodriguez [Saez Lab] writeup): [GSEA-MSigDB](https://www.gsea-msigdb.org), [6th Place Solution Writeup](https://www.kaggle.com/competitions/open-problems-single-cell-perturbations/discussion/461225)\n\n- HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F7b7e01384f681d7ed2624c8449810096%2F3.jpeg?generation=1703537496099980&alt=media)\n- HALLMARK_HYPOXIA\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F5fba7ce0faf2eeaaaa83e62a64a31d34%2F1.png?generation=1703537469280388&alt=media)\n- BIOCARTA_HIF_PATHWAY\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F15071851%2F83e41cd551d976c889154bf087b078ce%2F2.jpeg?generation=1703537481720642&alt=media)\n\nThese observations prompt further investigation into the biological mechanisms and underscore the need for careful consideration of potential data or analytical artifacts. The increased sensitivity of certain gene groups to external conditions warrants a closer look to fully understand their implications.\n\n[**View My Notebook**](https://www.kaggle.com/code/nikolenkosergei/op2-eda-housekeeping-genes)\n\n---\n\n*Note: \"Effects above the baseline\" refers to gene expressions exceeding the stability or deviations typically expected for housekeeping genes.*",
    "2576420": "cI have checked a few other families of genes that are related to stress response. \n1) Sirtuins, they take part in maintaining normal chromatin condensation state, in DNA damage response and repair, modulate oxidative stress and energy metabolism\n2) Genes associated with sirtuins - graph shows only genes related to regulation of metabolism\n3) Autophagy genes, usually elevated during stress as cell clears damaged proteins and organelles, and maintains metabolic balance\n\nHere is graph for 1)![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2Fe5b5494ec2f9c8c748042039004e976c%2FScreenshot%202023-12-29%20at%2020.55.17.png?generation=1703854579788691&alt=media)\nHere is for 2)![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2F633a0adea171d6b56a18c4eca2fae656%2FScreenshot%202023-12-26%20at%2000.31.47.png?generation=1703700722597563&alt=media)\nAnd here is for 3)![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2488571%2F601aa4c57aef71f02dc6d05c8d830352%2Fautophagy.png?generation=1703700752516429&alt=media)\n\nFor these group it does not seem that the expression is elevated. Interestingly that expression of 7 sirtuins is on the level with housekeeping genes.\n\nlink to notebook: https://www.kaggle.com/code/sankkan/op2-eda-housekeeping-genes-sirtuins-autophagy/edit/run/156987950"
  },
  "source": "meta"
}