Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_1841

UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (EC 6.3.2.10) (IMGterm)

CircVis
Functional Annotations (12)
Function System
UDP-N-acetylmuramyl pentapeptide synthase cog/ cog
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
regulation of cell shape go/ biological_process
UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity go/ molecular_function
cell division go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
murF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_1841
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_1841!

Warning: Synpcc7942_1841 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
1523 1.50e+05 Att.GTCaagAaAAa
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1524 6.40e+04 ACAGa.gTTGcTT.AcaacCtcA
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1525 1.60e+05 AAaGAtTTACAaAAaTTTACA
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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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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for Synpcc7942_1841

Synpcc7942_1841 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
UDP-N-acetylmuramyl pentapeptide synthase cog/ cog
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
regulation of cell shape go/ biological_process
UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity go/ molecular_function
cell division go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
murF tigr/ tigrfam
Module neighborhood information for Synpcc7942_1841

Synpcc7942_1841 has total of 63 gene neighbors in modules 1, 90
Gene neighbors (63)
Gene Common Name Description Module membership
Synpcc7942_0013 hypothetical protein 1, 31
Synpcc7942_0047 TPR repeat 1, 46
Synpcc7942_0054 hypothetical protein 1, 57
Synpcc7942_0107 Small GTP-binding protein domain 90, 107
Synpcc7942_0151 response regulator receiver modulated diguanylate cyclase (IMGterm) 1, 57
Synpcc7942_0195 hypothetical protein 1, 82
Synpcc7942_0196 "Beta-carotene 15,15'-dioxygenase (EC:1.13.11.43)" 1, 70
Synpcc7942_0230 hypothetical protein 1, 90
Synpcc7942_0266 Heat shock protein DnaJ-like 12, 90
Synpcc7942_0276 glycolate oxidase subunit GlcD (EC:1.1.3.15) 38, 90
Synpcc7942_0322 c-type cytochrome biogenesis protein 29, 90
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_0466 Cellulose synthase (UDP-forming) (EC:2.4.1.12) 1, 32
Synpcc7942_0512 conserved hypothetical protein YCF84 90, 117
Synpcc7942_0576 thiG thiazole-phosphate synthase (IMGterm) 1, 140
Synpcc7942_0630 hypothetical protein 1, 3
Synpcc7942_0764 "transcriptional regulator, XRE family (IMGterm)" 1, 2
Synpcc7942_0803 hypothetical protein 29, 90
Synpcc7942_0831 hypothetical protein (EC:2.7.6.5) 1, 90
Synpcc7942_0899 hypothetical protein 1, 14
Synpcc7942_0983 deoxyribose-phosphate aldolase (EC:4.1.2.4) 1, 57
Synpcc7942_0985 hypothetical protein 12, 90
Synpcc7942_1024 hypothetical protein 1, 118
Synpcc7942_1056 "transcriptional regulator, XRE family (IMGterm)" 5, 90
Synpcc7942_1102 hypothetical protein 1, 2
Synpcc7942_1120 hypothetical protein 1, 205
Synpcc7942_1302 hypothetical protein 1, 73
Synpcc7942_1385 hypothetical protein 1, 16
Synpcc7942_1395 hypothetical protein 1, 140
Synpcc7942_1406 ATPase (EC:3.6.3.30) 29, 90
Synpcc7942_1407 iron(III) ABC transporter permease protein 29, 90
Synpcc7942_1431 "Peptidylprolyl isomerase (EC:5.2.1.8, EC:5.2.1.8)" 1, 77
Synpcc7942_1504 hypothetical protein 1, 205
Synpcc7942_1527 nitrogen assimilation regulatory protein 1, 140
Synpcc7942_1704 hypothetical protein 1, 85
Synpcc7942_1731 hypothetical protein 1, 17
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_1930 hypothetical protein 1, 29
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_1957 cyclic nucleotide-binding domain (cNMP-BD) protein 1, 82
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_2201 alr alanine racemase (EC 5.1.1.1) (IMGterm) 1, 31
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_2318 hypothetical protein 1, 31
Synpcc7942_2324 glutathione synthase (EC 6.3.2.3) (IMGterm) 1, 140
Synpcc7942_2383 "Nucleotide binding protein, PINc" 29, 90
Synpcc7942_2395 hypothetical protein 90, 139
Synpcc7942_2429 outer membrane transport energization protein ExbB (TC 2.C.1.1.1) (IMGterm) 90, 118
Synpcc7942_2501 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54) (IMGterm) 90, 117
Synpcc7942_2572 hypothetical protein 1, 114
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.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

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.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

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.

Functions Tab

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.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

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.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

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.

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;
  • 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
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for Synpcc7942_1841
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

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;
  • 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
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend