Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_0348 recA

RecA protein (IMGterm)

CircVis
Functional Annotations (9)
Function System
RecA/RadA recombinase cog/ cog
nucleotide binding go/ molecular_function
DNA binding go/ molecular_function
ATP binding go/ molecular_function
DNA metabolic process go/ biological_process
DNA-dependent ATPase activity go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Homologous recombination kegg/ kegg pathway
tigrfam_recA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_0348
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_0348!

Warning: Synpcc7942_0348 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
1538 4.40e+01 CGATCGCc
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1539 3.40e+03 AAa.ctAAaAAattt
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1540 1.70e+04 CtGTtcaTtTCaGCTTG
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1547 9.80e+00 aaaaggCAATc
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1548 3.80e+04 AGcAGCtAagtC.gc.c.a
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1549 1.30e+05 AGCCgC
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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_0348

Synpcc7942_0348 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
RecA/RadA recombinase cog/ cog
nucleotide binding go/ molecular_function
DNA binding go/ molecular_function
ATP binding go/ molecular_function
DNA metabolic process go/ biological_process
DNA-dependent ATPase activity go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Homologous recombination kegg/ kegg pathway
tigrfam_recA tigr/ tigrfam
Module neighborhood information for Synpcc7942_0348

Synpcc7942_0348 has total of 53 gene neighbors in modules 6, 9
Gene neighbors (53)
Gene Common Name Description Module membership
Synpcc7942_0032 hypothetical protein 9, 33
Synpcc7942_0102 hypothetical protein 9, 87
Synpcc7942_0110 "transcriptional regulator, XRE family (IMGterm)" 6, 19
Synpcc7942_0213 hypothetical protein 9, 54
Synpcc7942_0217 phosphatase-like 9, 10
Synpcc7942_0348 recA RecA protein (IMGterm) 6, 9
Synpcc7942_0364 hypothetical protein 9, 107
Synpcc7942_0366 putative sulfate transporter 9, 57
Synpcc7942_0371 homoserine O-succinyltransferase (EC 2.3.1.46) (IMGterm) 6, 11
Synpcc7942_0390 Chromate transporter 9, 70
Synpcc7942_0394 phosphatidate cytidylyltransferase (EC:2.7.7.41) 6, 186
Synpcc7942_0476 clpS hypothetical protein 9, 87
Synpcc7942_0493 hypothetical protein 6, 11
Synpcc7942_0499 hydroxyneurosporene-O-methyltransferase (EC 2.1.1.-) (IMGterm) 6, 121
Synpcc7942_0564 ATPase 2, 9
Synpcc7942_0571 sugar (Glycoside-Pentoside-Hexuronide) transporter 6, 121
Synpcc7942_0572 hypothetical protein 6, 33
Synpcc7942_0703 "DNA processing protein DprA, putative" 6, 121
Synpcc7942_0796 hypothetical protein 9, 95
Synpcc7942_0827 cobalamin synthesis protein cobW-like 9, 77
Synpcc7942_0828 hypothetical protein 9, 50
Synpcc7942_1064 type I restriction-modification (EC:3.1.21.3) 9, 11
Synpcc7942_1065 DEAD/DEAH box helicase-like (EC:3.1.21.3) 9, 95
Synpcc7942_1156 hypothetical protein 6, 101
Synpcc7942_1157 hypothetical protein 6, 127
Synpcc7942_1214 Glutathione peroxidase (EC:1.11.1.9) 4, 9
Synpcc7942_1227 radC DNA replication and repair protein RadC (IMGterm) 6, 121
Synpcc7942_1295 Phospholipid/glycerol acyltransferase 6, 127
Synpcc7942_1382 diguanylate cyclase/phosphodiesterase (GGDEF & EAL domains) with PAS/PAC sensor(s) 9, 57
Synpcc7942_1404 "two component transcriptional regulator, winged helix family (IMGterm)" 9, 140
Synpcc7942_1509 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (EC 2.1.1.61) (IMGterm) 9, 95
Synpcc7942_1556 hypothetical protein 6, 101
Synpcc7942_1573 3-oxoacyl-(acyl-carrier protein) reductase (EC:1.1.1.47) 6, 54
Synpcc7942_1622 probable proteinase (EC:3.4.-) 9, 30
Synpcc7942_1643 diguanylate cyclase with GAF sensor (IMGterm) 9, 57
Synpcc7942_1669 "Potassium-translocating P-type ATPase, B subunit (EC:3.6.3.12)" 6, 101
Synpcc7942_1671 "potassium-transporting ATPase, C subunit (EC:3.6.3.12)" 6, 127
Synpcc7942_1991 large conductance mechanosensitive channel protein 6, 127
Synpcc7942_2078 phosphoglycerate mutase (EC:5.4.2.1) 6, 54
Synpcc7942_2080 Fructose-6-phosphate phosphoketolase (EC:4.1.2.22) 6, 127
Synpcc7942_2116 hypothetical protein 9, 79
Synpcc7942_2181 hypothetical protein 9, 26
Synpcc7942_2192 diguanylate cyclase (GGDEF domain) 9, 26
Synpcc7942_2253 "Glutamate--cysteine ligase, putative" 9, 19
Synpcc7942_2307 hypothetical protein 6, 101
Synpcc7942_2319 "putative plasmid maintenance system antidote protein, XRE family" 9, 70
Synpcc7942_2386 hydrogenase expression/formation protein HypD 6, 11
Synpcc7942_2387 hypothetical protein 6, 101
Synpcc7942_2388 Oxalate decarboxylase (EC:4.1.1.2) 6, 101
Synpcc7942_2406 glycine oxidase (EC 1.4.3.19) (IMGterm) 9, 87
Synpcc7942_2461 hypothetical protein (EC:3.5.3.12) 6, 101
Synpcc7942_2551 (NiFe) hydrogenase maturation protein HypF 6, 11
Synpcc7942_2598 hypothetical protein 9, 134
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_0348
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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