Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_2089

Thioredoxin domain 2

CircVis
Functional Annotations (4)
Function System
Predicted membrane protein cog/ cog
electron carrier activity go/ molecular_function
protein disulfide oxidoreductase activity go/ molecular_function
cell redox homeostasis go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_2089
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_2089!

Warning: Synpcc7942_2089 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
1871 1.00e-04 Ttg.caaAgtcTtGggtcAA
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1872 1.50e+02 ATctgggtTgAAcAACaCagA
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1873 8.60e+02 ATTGATGTTGTTCAAATAACCTAA
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1904 3.90e-02 TCTaGcggGGaATgctcAactT
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1905 6.60e+01 AaaAgtTgtTG
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1906 2.00e+04 CcgcaGCAaa.CCg
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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_2089

Synpcc7942_2089 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted membrane protein cog/ cog
electron carrier activity go/ molecular_function
protein disulfide oxidoreductase activity go/ molecular_function
cell redox homeostasis go/ biological_process
Module neighborhood information for Synpcc7942_2089

Synpcc7942_2089 has total of 34 gene neighbors in modules 117, 129
Gene neighbors (34)
Gene Common Name Description Module membership
Synpcc7942_0189 guaA GMP synthase (glutamine-hydrolyzing) (EC 6.3.5.2) (IMGterm) 117, 129
Synpcc7942_0360 hypothetical protein 38, 117
Synpcc7942_0452 hypothetical protein 117, 180
Synpcc7942_0512 conserved hypothetical protein YCF84 90, 117
Synpcc7942_0575 hypothetical protein 115, 117
Synpcc7942_0710 hypothetical protein 129, 184
Synpcc7942_0883 rpsJ SSU ribosomal protein S10P (IMGterm) 129, 200
Synpcc7942_0887 rpsL SSU ribosomal protein S12P (IMGterm) 29, 129
Synpcc7942_1015 methyl-accepting chemotaxis sensory transducer (IMGterm) 38, 117
Synpcc7942_1145 Glutaredoxin-related protein 117, 129
Synpcc7942_1146 "transcriptional regulator, BolA protein family (IMGterm)" 117, 129
Synpcc7942_1281 hypothetical protein 12, 117
Synpcc7942_1487 rpsD SSU ribosomal protein S4P (IMGterm) 129, 194
Synpcc7942_1616 hypothetical protein 117, 129
Synpcc7942_1679 photosystem II reaction center W protein 117, 139
Synpcc7942_1733 transcriptional regulator (IMGterm) 38, 117
Synpcc7942_1734 ferredoxin-thioredoxin reductase catalytic chain 107, 117
Synpcc7942_1735 Iron-regulated ABC transporter membrane component SufB (IMGterm) 5, 117
Synpcc7942_1782 L-threonine synthase (EC 4.2.3.1) (IMGterm) 107, 117
Synpcc7942_1985 hypothetical protein 117, 179
Synpcc7942_1986 "processing protease (EC:3.4.99.-, EC:3.4.24.64)" 38, 117
Synpcc7942_2019 hypothetical protein 90, 117
Synpcc7942_2072 heat shock protein GrpE 90, 117
Synpcc7942_2073 Heat shock protein Hsp70 90, 117
Synpcc7942_2074 Heat shock protein DnaJ 117, 129
Synpcc7942_2086 hypothetical protein 104, 129
Synpcc7942_2089 Thioredoxin domain 2 117, 129
Synpcc7942_2090 homoserine dehydrogenase (EC 1.1.1.3) (IMGterm) 35, 129
Synpcc7942_2113 ribose-phosphate pyrophosphokinase (EC:2.7.6.1) 29, 129
Synpcc7942_2331 cytochrome b6 115, 129
Synpcc7942_2332 cytochrome b6-f complex subunit 4 115, 129
Synpcc7942_2501 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54) (IMGterm) 90, 117
Synpcc7942_2541 rplS LSU ribosomal protein L19P (IMGterm) 117, 129
Synpcc7942_2583 hypothetical protein 117, 198
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_2089
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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