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P1k, 2022 pubs, revert filesize issue attempt 2
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‎about.html

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@@ -651,18 +651,19 @@ <h3>iModulonDB</h3>
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</ul>
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<ul class="list-group m-3 pt-2">
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<h3>Datasets on iModulonDB</h3>
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<a href="https://doi.org/10.1038/s41467-019-13483-w" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>E. coli</i> PRECISE-278:</b> Sastry, A.V., Gao, Y., Szubin, R. et al. The Escherichia coli transcriptome mostly consists of independently regulated modules. Nat Commun 10, 5536 (2019).</a>
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<a href="https://doi.org/10.1038/s41467-019-13483-w" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>E. coli</i> PRECISE-278 (1.0):</b> Sastry, A.V., Gao, Y., Szubin, R. et al. The Escherichia coli transcriptome mostly consists of independently regulated modules. Nat Commun 10, 5536 (2019).</a>
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<a href="https://doi.org/10.1073/pnas.2008413117" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>S. aureus Staph</i>PRECISE:</b> Poudel, S., Tsunemoto, H., Seif, Y. et al. Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators and role in key physiological responses. PNAS 117 (29) 17228-17239 (2020).</a>
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<a href="https://doi.org/10.1038/s41467-020-20153-9" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>B. subtilis</i> Microarray:</b> Rychel, K., Sastry, A.V., Palsson, B.O. Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome. Nat Commun 11, 6338 (2020).</a>
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<a href="https://doi.org/10.3389/fmicb.2021.753521" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>S. acidocaldarius</i> Modulome:</b> Chauhan, S.M., Poudel, S., Rychel, K. et al. Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile <i>Sulfolobus acidocaldarius</i>. Front. Microbiol. 12, 753521 (2021).</a>
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<a href="https://doi.org/10.1128/msphere.00033-22" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>M.tuberculosis</i> Modulome:</b> Yoo, R., Rychel, K., Sastry, A.V., et al. Machine Learning of All <i>Mycobacterium tuberculosis</i> H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection. mSphere. 7(2):e0003322 (2022).</a>
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<a href="https://doi.org/10.1093/nar/gkac187" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>P. aeruginosa aeru</i>PRECISE-364:</b> Rajput, A., Tsunemoto, H., Sastry, A.V. et al. Machine Learning of <i>Pseudomonas aeruginosa</i> transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators. Nucleic Acids Research 50, 3658 (2022)</a>
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<a href="https://doi.org/10.1016/j.ymben.2022.04.004" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>P. putida putida</i>PRECISE-321:</b> Lim, H.G., Rychel, K., Sastry, A.V. et al. Machine-learning from <i>Pseudomonas putida</i> KT2440 transcriptomes reveals its transcriptional regulatory network. Metab Eng 27, 297 (2022)</a>
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<a href="https://doi.org/10.1101/2022.04.04.487074" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>P. aeruginosa aeru</i>PRECISE-411:</b> Rajput, A., Tsunemoto, H., Sastry, A.V. et al. Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of <i>Pseudomonas aeruginosa</i>. Forthcoming.</a>
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<a href="https://doi.org/10.1101/2021.04.08.439047" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>E. coli</i> PRECISE-1k & Modulome:</b> Lamoureux, C.R., Decker, K.T., Sastry, A.V. et al. PRECISE 2.0 - an expanded high-quality RNA-seq compendium for Escherichia coli K-12 reveals high-resolution transcriptional regulatory structure. Forthcoming.</a>
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<a href="https://doi.org/10.1101/2022.01.11.475931" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>S. Enterica</i> Modulome:</b> Yuan, Y., Seif, Y., Rychel, K. et al. Pan-genomic analysis of transcriptional modules across Salmonella Typhimurium reveals the regulatory landscape of different strains. Forthcoming.</a>
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<a href="https://doi.org/10.1101/2021.07.01.450581" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>B. subtilis</i> Modulome:</b> Sastry, A.V., Poudel, S., Rychel, K., et al. Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks. Forthcoming.</a>
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<a href="https://www.biorxiv.org/content/10.1101/2022.08.04.502797v1" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>S. pyogenes</i> Modulome:</b> Hirose, Y., Poudel, S., Sastry, A.V., et al. Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins.Forthcoming.</a>
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<a href="https://doi.org/10.1093/nar/gkac743" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>P. aeruginosa aeru</i>PRECISE-411:</b> Rajput, A., Tsunemoto, H., Sastry, A.V. et al. Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of <i>Pseudomonas aeruginosa</i>. Nucleic Acids Research, 50, 9675 (2022).</a>
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<a href="https://doi.org/10.1128/msystems.00467-22" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>S. Enterica</i> Modulome:</b> Yuan, Y., Seif, Y., Rychel, K. et al. Pan-genomic analysis of transcriptional modules across Salmonella Typhimurium reveals the regulatory landscape of different strains. mSystems (2022).</a>
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<a href="https://doi.org/10.1101/2021.04.08.439047" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>E. coli</i> PRECISE-815 (2.0) & Modulome:</b> Lamoureux, C.R., Decker, K.T., Sastry, A.V. et al. PRECISE 2.0 - an expanded high-quality RNA-seq compendium for Escherichia coli K-12 reveals high-resolution transcriptional regulatory structure. BioRxiv.</a>
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<a href="https://doi.org/10.1101/2021.07.01.450581" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>B. subtilis</i> Modulome:</b> Sastry, A.V., Poudel, S., Rychel, K., et al. Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks. BioRxiv.</a>
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<a href="https://www.biorxiv.org/content/10.1101/2022.08.04.502797v1" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>S. pyogenes</i> Modulome:</b> Hirose, Y., Poudel, S., Sastry, A.V., et al. Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins. Forthcoming.</a>
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<a href="https://doi.org/10.1101/2021.04.08.439047" class="list-group-item list-group-item-action"><i class="fa-solid fa-newspaper pr-2"></i><b><i>E. coli</i> PRECISE-1K:</b> Lamoureux, C.R., Decker, K.T., Sastry, A.V., et al. A multi-scale transcriptional regulatory network knowledge base for <i>Escherichia coli</i>. Forthcoming.</a>
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‎index.html

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<div class="dropdown-menu">
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<span class="dropdown-item-text">
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<p class="im_head_meta_cat">ORGANISMS</p>
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<p class="im_head_meta_val">9</p>
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<p class="im_head_meta_val">11</p>
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<p class="im_head_meta_cat">DATASETS</p>
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<p class="im_head_meta_val">13</p><!--
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<p class="im_head_meta_val">16</p><!--
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<p class="im_head_meta_cat">UNIQUE SAMPLES</p>
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<p class="im_head_meta_val">3,976</p>
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<p class="im_head_meta_cat">UNIQUE CONDITIONS</p>
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<p class="im_head_meta_val">1,564</p>
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<p class="im_head_meta_cat">GENES</p>
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<p class="im_head_meta_val">24,680</p>-->
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<p class="im_head_meta_cat">iMODULONS</p>
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<p class="im_head_meta_val">1,422</p>
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<p class="im_head_meta_val">1,717</p>
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</span>
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<div id="e_coli" class="collapse" data-parent="#organismAccordion">
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<ul class="nav navbar-dark flex-column">
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<li class="nav-item dataset">
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<a class="nav-link active" href="dataset.html?organism=e_coli&dataset=precise1k">
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<i class="fa fa-star-o pr-2"></i>PRECISE-1K
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</a>
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</li>
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<i class="fa fa-star-o pr-2"></i>PRECISE 2.0
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<i class="fas fa-angle-right pl-2 pr-3"></i>PRECISE-815 (2.0)
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<i class="fas fa-angle-right pl-2 pr-3"></i>PRECISE 1.0
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<i class="fas fa-angle-right pl-2 pr-3"></i>PRECISE-278 (1.0)
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‎js/gene_table.js

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tf_column_start = 8
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}
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// adjust TF column start for missing data
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var columns_to_check = ["cog", "operon", "regulator"]
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for (i = 0; i < columns_to_check.length; i++) {
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if (!data[0].includes(columns_to_check[i])) {
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console.log(columns_to_check[i])
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tf_column_start = tf_column_start - 1
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}
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}
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for (j = tf_column_start; j < data[0].length - 1; j++) {
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columns.push({

‎organisms/e_coli/annotation/gene_files.zip

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