Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_0623

thioredoxin reductase (EC:1.8.1.9)

CircVis
Functional Annotations (10)
Function System
Thioredoxin reductase cog/ cog
thioredoxin-disulfide reductase activity go/ molecular_function
cytoplasm go/ cellular_component
electron transport go/ biological_process
glycerol ether metabolic process go/ biological_process
protein disulfide oxidoreductase activity go/ molecular_function
removal of superoxide radicals go/ biological_process
cell redox homeostasis go/ biological_process
Pyrimidine metabolism kegg/ kegg pathway
TRX_reduct tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_0623
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_0623!

Warning: Synpcc7942_0623 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
1739 2.90e+01 AgaaGTttgaTgTtaatggTTACA
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1740 1.20e+03 ttaGcgaTgTTGAGt.gTgtc
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1741 8.30e+03 TcatgAccccTcTtGTCAtcC
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1979 1.20e+00 aAacAatccTGAaAtTATta
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1980 3.10e+03 GAa.caA.aGtgAaaTgaTga
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1981 2.40e+04 gCTgtcg.tagCGCaGgtcaa
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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_0623

Synpcc7942_0623 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Thioredoxin reductase cog/ cog
thioredoxin-disulfide reductase activity go/ molecular_function
cytoplasm go/ cellular_component
electron transport go/ biological_process
glycerol ether metabolic process go/ biological_process
protein disulfide oxidoreductase activity go/ molecular_function
removal of superoxide radicals go/ biological_process
cell redox homeostasis go/ biological_process
Pyrimidine metabolism kegg/ kegg pathway
TRX_reduct tigr/ tigrfam
Module neighborhood information for Synpcc7942_0623

Synpcc7942_0623 has total of 55 gene neighbors in modules 73, 154
Gene neighbors (55)
Gene Common Name Description Module membership
Synpcc7942_0042 rpmB LSU ribosomal protein L28P (IMGterm) 40, 73
Synpcc7942_0052 hypothetical protein 44, 73
Synpcc7942_0080 probable ABC transporter permease protein 154, 198
Synpcc7942_0169 "glutamate-ammonia ligase, glutamine synthetase type III (EC:6.3.1.2)" 45, 154
Synpcc7942_0221 glk glucokinase (EC 2.7.1.2) (IMGterm) 73, 77
Synpcc7942_0240 hypothetical protein 73, 107
Synpcc7942_0241 23S rRNA m(5)U-1939 methyltransferase (EC 2.1.1.-) (IMGterm) 73, 131
Synpcc7942_0387 hypothetical protein 8, 154
Synpcc7942_0425 hypothetical protein 21, 73
Synpcc7942_0465 hypothetical protein 32, 73
Synpcc7942_0494 hypothetical protein 21, 154
Synpcc7942_0496 hypothetical protein 154, 177
Synpcc7942_0497 hypothetical protein 154, 155
Synpcc7942_0501 Nucleoside-diphosphate-sugar epimerase-like 154, 177
Synpcc7942_0548 hypothetical protein 73, 156
Synpcc7942_0623 thioredoxin reductase (EC:1.8.1.9) 73, 154
Synpcc7942_0624 light dependent period 8, 73
Synpcc7942_0625 Single-stranded nucleic acid binding R3H 73, 140
Synpcc7942_0658 hypothetical protein 73, 110
Synpcc7942_0771 hypothetical protein (EC:2.5.1.18) 73, 140
Synpcc7942_0801 Superoxide dismutase (EC:1.15.1.1) 40, 73
Synpcc7942_0804 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase (EC 1.1.1.262) (IMGterm) 154, 177
Synpcc7942_0833 hypothetical protein 8, 154
Synpcc7942_0843 hypothetical protein 46, 73
Synpcc7942_0880 hypothetical protein 73, 154
Synpcc7942_0988 conserved hypothetical protein YCF54 55, 154
Synpcc7942_1167 hypothetical protein 16, 73
Synpcc7942_1257 chloride channel-like 8, 154
Synpcc7942_1258 hypothetical protein 8, 154
Synpcc7942_1289 putative modulator of DNA gyrase 154, 155
Synpcc7942_1297 Malate dehydrogenase (oxaloacetate decarboxylating) (EC:1.1.1.38) 14, 73
Synpcc7942_1302 hypothetical protein 1, 73
Synpcc7942_1303 hypothetical protein 36, 154
Synpcc7942_1361 hypothetical protein 36, 154
Synpcc7942_1409 iron transport system substrate-binding protein 40, 73
Synpcc7942_1624 "riboflavin synthase, alpha subunit (EC:2.5.1.9)" 131, 154
Synpcc7942_1673 hypothetical protein 73, 131
Synpcc7942_1676 hypothetical protein 8, 154
Synpcc7942_1862 hypothetical protein 73, 160
Synpcc7942_1866 hypothetical protein 35, 73
Synpcc7942_1942 bacterioferritin comigratory protein-like (EC:1.11.1.15) 36, 73
Synpcc7942_1952 hypothetical protein 73, 77
Synpcc7942_2005 flm3 region hypothetical protein 4 36, 154
Synpcc7942_2038 "transcriptional regulator, XRE family with cupin sensor domain" 73, 112
Synpcc7942_2067 hypothetical protein 74, 154
Synpcc7942_2125 hypothetical protein 85, 154
Synpcc7942_2281 hypothetical protein 16, 73
Synpcc7942_2309 thioredoxin peroxidase (EC:1.11.1.15) 40, 73
Synpcc7942_2347 hypothetical protein 154, 156
Synpcc7942_2402 agmatine deiminase (EC 3.5.3.12) (IMGterm) 16, 73
Synpcc7942_2466 "two component transcriptional regulator, winged helix family (IMGterm)" 2, 73
Synpcc7942_2560 "Acetyltransferase, GNAT family (IMGterm)" 85, 154
Synpcc7942_2574 ATPase 85, 154
Synpcc7942_2575 Mn transporter MntC 73, 154
Synpcc7942_2608 hypothetical protein 8, 73
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_0623
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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