Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_2490 miaA

tRNA delta(2)-isopentenylpyrophosphate transferase (EC:2.5.1.75)

CircVis
Functional Annotations (9)
Function System
tRNA delta(2)-isopentenylpyrophosphate transferase cog/ cog
dimethylallyltranstransferase activity go/ molecular_function
ATP binding go/ molecular_function
tRNA processing go/ biological_process
biosynthetic process go/ biological_process
tRNA dimethylallyltransferase activity go/ molecular_function
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
miaA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_2490
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_2490!

Warning: Synpcc7942_2490 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
1877 1.20e+02 tAgagtctTca.gaTTtTT
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1878 1.10e+03 ca.AAAGCcGt
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1879 5.40e+03 aagcAacgCaggcTg
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2126 1.40e-01 cCtgCTgC
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2127 9.10e+03 CacgGctGG.T
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2128 1.30e+04 CgCAgctTTTcG
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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_2490

Synpcc7942_2490 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
tRNA delta(2)-isopentenylpyrophosphate transferase cog/ cog
dimethylallyltranstransferase activity go/ molecular_function
ATP binding go/ molecular_function
tRNA processing go/ biological_process
biosynthetic process go/ biological_process
tRNA dimethylallyltransferase activity go/ molecular_function
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
miaA tigr/ tigrfam
Module neighborhood information for Synpcc7942_2490

Synpcc7942_2490 has total of 38 gene neighbors in modules 120, 203
Gene neighbors (38)
Gene Common Name Description Module membership
Synpcc7942_0066 hypothetical protein 64, 203
Synpcc7942_0067 probable permease protein of ABC transporter 64, 203
Synpcc7942_0150 Dolichyl-phosphate beta-D-mannosyltransferase (EC:2.4.1.83) 65, 203
Synpcc7942_0238 hypothetical protein 91, 120
Synpcc7942_0239 cytochrome C6 soluble cytochrome f 120, 161
Synpcc7942_0246 L-glutamate-binding protein / L-aspartate-binding protein / neutral amino acid-binding protein (IMGterm) 104, 120
Synpcc7942_0261 [SSU ribosomal protein S18P]-alanine acetyltransferase (EC 2.3.1.128) (IMGterm) 88, 203
Synpcc7942_0272 uroporphyrinogen-III synthase (EC 4.2.1.75) (IMGterm) 143, 203
Synpcc7942_0362 hypothetical protein 120, 184
Synpcc7942_0588 purT formate-dependent phosphoribosylglycinamide formyltransferase (EC 6.3.4.-) (IMGterm) 46, 120
Synpcc7942_0602 hypothetical protein 120, 203
Synpcc7942_0671 hypothetical protein 120, 179
Synpcc7942_0811 "sodium/proton antiporter, CPA1 family (TC 2.A.36) (IMGterm)" 143, 203
Synpcc7942_0848 uvrA Excinuclease ABC subunit A (IMGterm) 120, 203
Synpcc7942_0929 lpxC UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) (IMGterm) 120, 186
Synpcc7942_1030 histidinol phosphate aminotransferase apoenzyme (EC 2.6.1.9) (IMGterm) 93, 120
Synpcc7942_1169 oligopeptide-binding protein of oligopeptide ABC transporter 64, 203
Synpcc7942_1244 ATPase 63, 203
Synpcc7942_1360 cell envelope-related transcriptional attenuator (IMGterm) 124, 203
Synpcc7942_1482 hypothetical protein 143, 203
Synpcc7942_1500 prmA [LSU ribosomal protein L11P]-lysine N-methyltransferase (EC 2.1.1.-) (IMGterm) 59, 120
Synpcc7942_1596 probable short-chain dehydrogenase 120, 138
Synpcc7942_1632 hypothetical protein 120, 167
Synpcc7942_1658 hypothetical protein 120, 165
Synpcc7942_1717 glycolate oxidase subunit (Fe-S) protein 104, 203
Synpcc7942_1763 inositol monophosphate family protein (EC:3.1.3.25) 14, 120
Synpcc7942_1778 hypothetical protein 64, 203
Synpcc7942_1825 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5) (IMGterm) 120, 143
Synpcc7942_1834 hypothetical protein 139, 203
Synpcc7942_1863 "modification methylase, HemK family (EC:2.1.1.-)" 167, 203
Synpcc7942_1881 L-aspartate oxidase (EC 1.4.3.16) (IMGterm) 118, 120
Synpcc7942_1988 hypothetical protein 143, 203
Synpcc7942_2052 probable oligopeptides ABC transporter permease protein 91, 203
Synpcc7942_2106 nitrate transport permease 83, 120
Synpcc7942_2408 hypothetical protein 120, 188
Synpcc7942_2425 chaperon-like protein for quinone binding in photosystem II 120, 138
Synpcc7942_2490 miaA tRNA delta(2)-isopentenylpyrophosphate transferase (EC:2.5.1.75) 120, 203
Synpcc7942_2546 hypothetical protein 91, 120
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_2490
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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