Organism : Synechococcus elongatus PCC 7942
| Module List :
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Synpcc7942_0266
Heat shock protein DnaJ-like
Functional Annotations (3)
Function | System |
---|---|
protein folding | go/ biological_process |
heat shock protein binding | go/ molecular_function |
unfolded protein binding | go/ molecular_function |
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Motif information (de novo identified motifs for modules)
There are 6 motifs predicted.
Motif Id | e-value | Consensus | Motif Logo |
---|---|---|---|
1556 | 1.00e+04 | aTGa.AGAgAAacT |
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1557 | 1.40e+05 | GCCtGAAtCAC |
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1558 | 9.10e+04 | TTtcCcatgtTgtaGcT.CT |
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1790 | 6.50e+01 | TtTTCcagtgttGggtgaTcT |
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1791 | 1.80e+02 | AttGCCCCGt |
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1792 | 4.20e+01 | aAGCaGCaaTC |
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Functional Enrichment for Synpcc7942_0266
Function | System |
---|---|
protein folding | go/ biological_process |
heat shock protein binding | go/ molecular_function |
unfolded protein binding | go/ molecular_function |
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Module neighborhood information for Synpcc7942_0266
Gene | Common Name | Description | Module membership |
---|---|---|---|
Synpcc7942_0076 | "amino acid ABC transporter substrate-binding protein, PAAT family (TC 3.A.1.3.-) (IMGterm)" | 12, 163 | |
Synpcc7942_0092 | hypothetical protein | 2, 12 | |
Synpcc7942_0107 | Small GTP-binding protein domain | 90, 107 | |
Synpcc7942_0230 | hypothetical protein | 1, 90 | |
Synpcc7942_0258 | hypothetical protein | 12, 41 | |
Synpcc7942_0266 | Heat shock protein DnaJ-like | 12, 90 | |
Synpcc7942_0276 | glycolate oxidase subunit GlcD (EC:1.1.3.15) | 38, 90 | |
Synpcc7942_0281 | "probable glycosyltransferase (EC:2.7.8.-, EC:2.7.8.-)" | 12, 46 | |
Synpcc7942_0322 | c-type cytochrome biogenesis protein | 29, 90 | |
Synpcc7942_0349 | hypothetical protein | 12, 38 | |
Synpcc7942_0365 | response regulator receiver domain protein (CheY-like) | 12, 90 | |
Synpcc7942_0400 | "anthranilate synthase, component II (EC 4.1.3.27) (IMGterm)" | 90, 184 | |
Synpcc7942_0401 | diacylglycerol kinase (EC 2.7.1.107) (IMGterm) | 11, 90 | |
Synpcc7942_0462 | hypothetical protein | 12, 130 | |
Synpcc7942_0463 | protein tyrosine phosphatase (IMGterm) | 12, 130 | |
Synpcc7942_0512 | conserved hypothetical protein YCF84 | 90, 117 | |
Synpcc7942_0803 | hypothetical protein | 29, 90 | |
Synpcc7942_0831 | hypothetical protein (EC:2.7.6.5) | 1, 90 | |
Synpcc7942_0873 | hypothetical protein | 12, 44 | |
Synpcc7942_0886 | SSU ribosomal protein S7P (IMGterm) | 12, 141 | |
Synpcc7942_0985 | hypothetical protein | 12, 90 | |
Synpcc7942_1056 | "transcriptional regulator, XRE family (IMGterm)" | 5, 90 | |
Synpcc7942_1224 | ABC-transporter membrane fusion protein | 12, 13 | |
Synpcc7942_1281 | hypothetical protein | 12, 117 | |
Synpcc7942_1287 | VCBS | 12, 186 | |
Synpcc7942_1406 | ATPase (EC:3.6.3.30) | 29, 90 | |
Synpcc7942_1407 | iron(III) ABC transporter permease protein | 29, 90 | |
Synpcc7942_1478 | cytochrome CytM | 12, 122 | |
Synpcc7942_1561 | hypothetical protein | 12, 80 | |
Synpcc7942_1562 | ADP-ribosylglycohydrolase-like (EC:3.2.-) | 12, 92 | |
Synpcc7942_1578 | Sec-independent protein translocase TatC (IMGterm) | 12, 72 | |
Synpcc7942_1755 | hypothetical protein | 12, 46 | |
Synpcc7942_1806 | bacterioferritin comigratory protein (EC:1.11.1.15) | 13, 90 | |
Synpcc7942_1841 | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (EC 6.3.2.10) (IMGterm) | 1, 90 | |
Synpcc7942_1907 | Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase (EC 1.14.13.81) (IMGterm) | 29, 90 | |
Synpcc7942_1931 | "probable serine/threonine protein phosphatase (EC:3.1.3.16, EC:3.1.3.16)" | 41, 90 | |
Synpcc7942_1936 | hypothetical protein | 13, 90 | |
Synpcc7942_1977 | NADH dehydrogenase subunit L (EC 1.6.5.3) (IMGterm) | 12, 194 | |
Synpcc7942_1983 | three-step phytoene desaturase (EC 1.3.99.-) / zeta-carotene desaturase (EC 1.3.99.-) (IMGterm) | 12, 140 | |
Synpcc7942_2019 | hypothetical protein | 90, 117 | |
Synpcc7942_2056 | hypothetical protein | 90, 94 | |
Synpcc7942_2072 | heat shock protein GrpE | 90, 117 | |
Synpcc7942_2073 | Heat shock protein Hsp70 | 90, 117 | |
Synpcc7942_2130 | hypothetical protein | 90, 107 | |
Synpcc7942_2171 | starvation induced DNA binding protein | 38, 90 | |
Synpcc7942_2202 | HNH nuclease | 13, 90 | |
Synpcc7942_2240 | conserved hypothetical protein YCF52 | 38, 90 | |
Synpcc7942_2282 | GAF sensor signal transduction histidine kinase (EC 2.7.13.3) (IMGterm) | 38, 90 | |
Synpcc7942_2302 | hypothetical protein | 43, 90 | |
Synpcc7942_2338 | hypothetical protein | 5, 12 | |
Synpcc7942_2383 | "Nucleotide binding protein, PINc" | 29, 90 | |
Synpcc7942_2395 | hypothetical protein | 90, 139 | |
Synpcc7942_2423 | glucose inhibited division protein A | 12, 38 | |
Synpcc7942_2424 | hypothetical protein | 12, 132 | |
Synpcc7942_2429 | outer membrane transport energization protein ExbB (TC 2.C.1.1.1) (IMGterm) | 90, 118 | |
Synpcc7942_2438 | "putative CheA signal transduction histidine kinase, no good domain identification" | 12, 41 | |
Synpcc7942_2460 | DNA-cytosine methyltransferase (EC:2.1.1.37) | 12, 31 | |
Synpcc7942_2501 | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54) (IMGterm) | 90, 117 |
Gene Page Help
Network Tab
If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.
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Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
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For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.
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Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.
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Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.
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Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.
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CircVis
Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;![](/static/images/help_images/circvis-help.png)
- 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
- 2. Source gene
- 3. Target genes (other module members)
- 4. Interactions between source and target genes for a particular module
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In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.