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A SmartTable is a collection of BioCyc objects, such as genes or metabolites, together with associated data, that can be created, edited, manipulated, and shared on the web.[SmartTables Documentation] [Directory of SmartTables Users]
 
SmartTable |
Description | Organism | Type | Size |
Owner |
Update Time | |
|---|---|---|---|---|---|---|---|
| 1 | Genes of E. coli K-12 substr. MG1655 with TAG stop codon | Escherichia coli K-12 substr. MG1655 | all-genes | 316 | Gabriella Machado | 2 days ago 11:27 am | |
| 2 | Cyanobacteria List: Curated Cyanobacterial Databases | A list of the Tier 2 (curated) BioCyc cyanobacterial databases.
| ocelot-kb | 5 | Peter Karp | Sun Sep 24 2023 08:45 pm | |
| 3 | New SmartTable with nhaA | Escherichia coli K-12 substr. MG1655 | all-genes | 6 | YIMING HUANG | Sun Sep 10 2023 09:55 pm | |
| 4 | Enriched from Dark Green & Purple Transcription Genes (12 Results) | Abiotrophia defectiva ATCC 49176 | pathways | 12 | Olivia Noble | Fri Sep 08 2023 01:26 pm | |
| 5 | Copy of all gene products that have one of the following evidence codes: EV-COMP, EV-IC, EV-EXP | Synechocystis sp. PCC 6803 substr. Kazusa | all-genes | 322 | Lisa Moore | Fri Sep 08 2023 01:20 pm | |
| 6 | SmT shared: genes-without-TUs SmartTable - 2023-08-28T17:59:16 -8 | Escherichia coli K-12 substr. MG1655 | all-genes | 158 | helio sun | Mon Aug 28 2023 08:28 pm | |
| 7 | GSE71562 RNA-Seq anaerobic-aerobic transition | This SmartTable is an example generated via the Cellular Dashboard. The data is derived from von Wulffen et al, PMID 27384956, and has been normalized using the TPM approach. To view this dataset using the Cellular Dashboard, see http://biocyc.org/dashboard/dashboard.html?st=samo-463-3699298732. | Escherichia coli K-12 substr. MG1655 | gene-fragments, symbol, all-genes | 4231 | Suzanne Paley | Fri Aug 18 2023 09:49 am |
| 8 | Genes categorias 1, 4A e 5A | Escherichia coli K-12 substr. MG1655 | all-genes | 68 | Gabriella Machado | Mon Aug 07 2023 02:27 pm | |
| 9 | updated 383 genes 417 EC numbers | Methanocaldococcus jannaschii DSM 2661 | reactions, proteins | 417 | Christos Ouzounis | Fri Aug 04 2023 11:02 am | |
| 10 | Sequences of Promoters regulated by RpoS and RpoD | How this SmartTable was generated:
1) From the source table, I clicked on the plus icon for the Recognized-Promoters to get a new ST w/ the promoters (you could also have started from the Special ST for all promoters, added the property Binds-Sigma-Factor and filtered based on that column).
2) Added the transform column "Sequence - coordinates of DNA region". Unfortunately that just gives you a sequence region one base long, the transcription start site, so it has to be extended.
3) Selected the sequence region column, and added the transform column "Sequence - modify coordinates of DNA region". I added 60 bases upstream and 25 bases downstream, which is what we show when we draw our promoter sequences on our transcription-unit pages.
4) I selected the new region column and added the transform "Sequence - sequence of DNA region".
5) I tweaked the column names to make them more comprehensible.
| Escherichia coli K-12 substr. MG1655 | promoters | 2241 | Suzanne Paley | Tue Jul 18 2023 08:42 am |
| 11 | Genes regulated by RpoS and RpoD | To get a list of all genes regulated by sigma S: From rpoS, I added a transform to the gene product. Selected the gene product column and added the property Recognized-Promoters. Selected that column and added the transform "transcription units of promoter". Selected that column and added the transform "Genes of transcription unit". I then added a new row, entered rpoD (selected "rpoD (All Genes)" from autocomplete options), and all its other columns were filled in automatically. | Escherichia coli K-12 substr. MG1655 | all-genes | 2 | Suzanne Paley | Mon Jul 17 2023 08:27 am |
| 12 | Location, Copy-Number, esentiality, All genes of E. coli K-12 substr. MG1655 | Escherichia coli K-12 substr. MG1655 | all-genes | 4706 | Tatsuya Sakaguchi | Tue Jun 27 2023 06:04 am | |
| 13 | New SmartTable - 2023-06-07T06:46:36 -8 | Saccharomyces cerevisiae S288c | all-genes | 27 | t.kosir | Wed Jun 07 2023 06:51 am | |
| 14 | Copy of All genes of E. coli K-12 substr. MG1655 | Escherichia coli K-12 substr. MG1655 | all-genes | 4746 | 家坤 朱 | Tue May 23 2023 08:20 pm | |
| 15 | All transporters of S. cerevisiae S288c | Saccharomyces cerevisiae S288c | all-genes | 349 | Mohamed Ouertani | Wed May 17 2023 12:04 pm | |
| 16 | All transporters of B. subtilis subtilis 168 | Bacillus subtilis subtilis 168 | all-genes | 633 | Mohamed Ouertani | Wed May 17 2023 12:00 pm | |
| 17 | All transporters of E. coli K-12 substr. MG1655 | Escherichia coli K-12 substr. MG1655 | string, all-genes | 480 | Mohamed Ouertani | Tue May 16 2023 11:56 pm | |
| 18 | Bacillus subtilis 168 amino acid biosynthesis | Bacillus subtilis subtilis 168 | pathways | 33 | Kelsie Nauta | Tue Apr 25 2023 12:40 am | |
| 19 | oxygenic photosynthesis of 10 cyanobacteria | Synechococcus elongatus PCC 7942, Neosynechococcus sphagnicola CAUP A 1101, Mastigocladopsis repens PCC 10914, Leptolyngbya frigida ULC18, Leptolyngbya boryana dg5, Calothrix brevissima NIES-22, Anabaena azotica FACHB-119, Aliterella atlantica CENA595, Acaryochloris sp. CCMEE 5410, Acaryochloris marina MBIC11017 | organisms | 10 | nitsan catalan | Sat Apr 01 2023 06:15 pm | |
| 20 | Locomotion genes in other PGDBs | Synechococcus elongatus PCC 7942 | all-genes | 45 | Stas Malavin | Fri Mar 31 2023 04:04 pm |