Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_2091

"NAD(P)H dehydrogenase, subunit NdhF3 family (EC:1.6.5.3)"

CircVis
Functional Annotations (6)
Function System
NADH:ubiquinone oxidoreductase subunit 5 (chain L)/Multisubunit Na+/H+ antiporter, MnhA subunit cog/ cog
NADH dehydrogenase (ubiquinone) activity go/ molecular_function
ATP synthesis coupled electron transport go/ biological_process
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
ndhF3_CO2 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_2091
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_2091!

Warning: Synpcc7942_2091 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
1652 2.10e-02 TcaatgtTtTtcaTt
Loader icon
1653 1.30e+00 A.ag.aTTgat.tctAGattttTa
Loader icon
1654 1.60e+02 AttAAtttTTA
Loader icon
1913 4.90e+02 ctA.GATTt.T.aA
Loader icon
1914 1.10e+04 tTgc.CtGgtcAaac
Loader icon
1915 4.20e+04 TGCcG.gccTg
Loader icon
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_2091

Synpcc7942_2091 is enriched for 6 functions in 3 categories.
Module neighborhood information for Synpcc7942_2091

Synpcc7942_2091 has total of 46 gene neighbors in modules 44, 132
Gene neighbors (46)
Gene Common Name Description Module membership
Synpcc7942_0051 TPR repeat 44, 104
Synpcc7942_0052 hypothetical protein 44, 73
Synpcc7942_0053 hypothetical protein 41, 44
Synpcc7942_0161 hypothetical protein 132, 138
Synpcc7942_0398 hypothetical protein 115, 132
Synpcc7942_0578 UDP-sulfoquinovose synthase (EC 3.13.1.1) (IMGterm) 115, 132
Synpcc7942_0655 photosystem II D2 protein (photosystem q(a) protein) 132, 145
Synpcc7942_0656 photosystem II 44 kDa subunit reaction center protein 132, 145
Synpcc7942_0850 hypothetical protein 132, 161
Synpcc7942_0873 hypothetical protein 12, 44
Synpcc7942_0893 photosystem q(b) protein 115, 132
Synpcc7942_0971 hypothetical protein 13, 132
Synpcc7942_1196 hypothetical protein 132, 145
Synpcc7942_1236 nitrate transport ATP-binding subunits C and D (EC:3.6.3.-) 115, 132
Synpcc7942_1237 nitrate transport ATP-binding subunits C and D 115, 132
Synpcc7942_1238 nitrate transport permease 115, 132
Synpcc7942_1239 ABC-type nitrate/nitrite transport system substrate-binding protein 115, 132
Synpcc7942_1240 nirA assimilatory nitrite reductase (ferredoxin) precursor (EC 1.7.7.1) (IMGterm) 115, 132
Synpcc7942_1343 NADH dehydrogenase subunit H (EC 1.6.5.3) (IMGterm) 81, 132
Synpcc7942_1345 NADH dehydrogenase subunit J (EC 1.6.5.3) (IMGterm) 81, 132
Synpcc7942_1368 hypothetical protein 13, 44
Synpcc7942_1390 protein kinase C inhibitor 35, 132
Synpcc7942_1470 "multisubunit sodium/proton antiporter, MrpG subunit (TC 2.A.63.1) (IMGterm)" 31, 44
Synpcc7942_1471 hypothetical protein 2, 44
Synpcc7942_1473 "multisubunit sodium/proton antiporter, MrpD subunit (TC 2.A.63.1) (IMGterm)" 44, 78
Synpcc7942_1474 "multisubunit sodium/proton antiporter, MrpC subunit (TC 2.A.63.1) (IMGterm)" 31, 44
Synpcc7942_1475 sodium-dependent bicarbonate transporter 31, 44
Synpcc7942_1476 hypothetical protein 31, 44
Synpcc7942_1486 Protein of unknown function DUF37 132, 160
Synpcc7942_1766 cytochrome bd plastoquinol oxidase subunit 2 apoprotein (EC 1.10.3.-) (IMGterm) 44, 92
Synpcc7942_1851 assimilatory nitrite reductase (ferredoxin) precursor (EC 1.7.7.1) (IMGterm) 44, 167
Synpcc7942_1852 cobH precorrin-8X methylmutase (EC 5.4.1.2) (IMGterm) 44, 167
Synpcc7942_1888 hypothetical protein 44, 160
Synpcc7942_1948 hypothetical protein 42, 132
Synpcc7942_2050 hypothetical protein 44, 46
Synpcc7942_2091 "NAD(P)H dehydrogenase, subunit NdhF3 family (EC:1.6.5.3)" 44, 132
Synpcc7942_2092 NADH dehydrogenase subunit M (EC 1.6.5.3) (IMGterm) 44, 132
Synpcc7942_2093 CO2 hydration protein 44, 132
Synpcc7942_2094 Beta-Ig-H3/fasciclin 44, 132
Synpcc7942_2139 probable glutathione S-transferase (EC:2.5.1.18) 31, 44
Synpcc7942_2175 transport system substrate-binding protein 72, 132
Synpcc7942_2359 "sodium/proton antiporter NhaS3, CPA2 family (TC 2.A.37.2.4) (IMGterm)" 44, 63
Synpcc7942_2360 N-acetylmuramoyl-L-alanine amidase (EC:3.5.1.28) 44, 194
Synpcc7942_2361 glutamate racemase (EC 5.1.1.3) (IMGterm) 44, 130
Synpcc7942_2424 hypothetical protein 12, 132
Synpcc7942_2443 "phosphate ABC transporter membrane protein 1, PhoT family (TC 3.A.1.7.1) (IMGterm)" 44, 165
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_2091
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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