Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_1082

"ATPase, E1-E2 type (EC:3.6.3.8)"

CircVis
Functional Annotations (8)
Function System
Cation transport ATPase cog/ cog
ATP binding go/ molecular_function
cation transport go/ biological_process
metabolic process go/ biological_process
ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism go/ molecular_function
proton transport go/ biological_process
membrane go/ cellular_component
ATPase_P-type tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_1082
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_1082!

Warning: Synpcc7942_1082 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
1886 4.80e-03 .CGATCGC
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1887 7.30e+02 AttAtCaTcaaAagCAatGcCAgC
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1888 2.90e+03 ActAatgCAActgccaAGgaATgA
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2072 1.00e-06 TAa.TcAggTaAA.ccggca.Tca
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2073 0.00e+00 tTcatTA.A.CttGtcgtcGtgAa
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2074 2.80e+00 GacCgAAgGAa.aTTgtTcAa
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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_1082

Synpcc7942_1082 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Cation transport ATPase cog/ cog
ATP binding go/ molecular_function
cation transport go/ biological_process
metabolic process go/ biological_process
ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism go/ molecular_function
proton transport go/ biological_process
membrane go/ cellular_component
ATPase_P-type tigr/ tigrfam
Module neighborhood information for Synpcc7942_1082

Synpcc7942_1082 has total of 39 gene neighbors in modules 123, 185
Gene neighbors (39)
Gene Common Name Description Module membership
Synpcc7942_0061 "CDP-glucose 4,6-dehydratase (EC:4.2.1.45)" 85, 185
Synpcc7942_0062 glucose-1-phosphate cytidylyltransferase (EC:2.7.7.33) 85, 185
Synpcc7942_0129 "Resolvase, RNase H-like fold" 19, 123
Synpcc7942_0524 hypothetical protein 22, 123
Synpcc7942_0574 hypothetical protein 30, 123
Synpcc7942_0666 Heat shock protein DnaJ-like 123, 126
Synpcc7942_0683 potassium channel protein 22, 123
Synpcc7942_0767 hypothetical protein 32, 185
Synpcc7942_0822 permease protein of oligopeptide ABC 118, 185
Synpcc7942_0837 hypothetical protein 185, 192
Synpcc7942_0838 Elongator protein 3/MiaB/NifB 185, 192
Synpcc7942_0839 "Nitrilase (EC:3.5.5.7, EC:3.5.5.1)" 185, 192
Synpcc7942_0840 hypothetical protein 185, 192
Synpcc7942_0841 putative flavoprotein involved in K+ transport 123, 185
Synpcc7942_0907 hypothetical protein 113, 185
Synpcc7942_1073 rph RNAse PH (EC 2.7.7.56) (IMGterm) 46, 185
Synpcc7942_1082 "ATPase, E1-E2 type (EC:3.6.3.8)" 123, 185
Synpcc7942_1097 hypothetical protein 123, 187
Synpcc7942_1128 hypothetical protein 185, 196
Synpcc7942_1155 hypothetical protein 123, 179
Synpcc7942_1159 "transcriptional regulator, MarR family (IMGterm)" 85, 185
Synpcc7942_1160 hypothetical protein 19, 185
Synpcc7942_1166 hypothetical protein 19, 123
Synpcc7942_1326 transcription-repair coupling factor (IMGterm) 40, 123
Synpcc7942_1462 imelysin. Metallo peptidase. MEROPS family M75 (IMGterm) 151, 185
Synpcc7942_1580 hypothetical protein 93, 185
Synpcc7942_1581 "Peptidase M14, carboxypeptidase A" 77, 185
Synpcc7942_1785 hypothetical protein 46, 123
Synpcc7942_1791 hypothetical protein (EC:1.1.5.2) 123, 126
Synpcc7942_1870 Secretion protein HlyD 123, 126
Synpcc7942_2025 probable glycosyltransferase 17, 185
Synpcc7942_2045 condensin subunit Smc (IMGterm) 65, 123
Synpcc7942_2097 hypothetical protein 123, 176
Synpcc7942_2198 hypothetical protein 55, 123
Synpcc7942_2298 ruvA Holliday junction DNA helicase subunit RuvA (IMGterm) 68, 185
Synpcc7942_2325 PBS lyase HEAT-like repeat 123, 176
Synpcc7942_2357 hypothetical protein 123, 151
Synpcc7942_2379 "Phosphomethylpyrimidine kinase (EC:2.7.4.7, EC:2.7.1.49)" 34, 123
Synpcc7942_2571 "Penicillin-binding protein 1A (EC:3.4.-, EC:2.4.1.-)" 88, 123
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_1082
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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