Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_2235 trmD

tRNA (Guanine37-N(1)-) methyltransferase (EC 2.1.1.31) (IMGterm)

CircVis
Functional Annotations (5)
Function System
tRNA-(guanine-N1)-methyltransferase cog/ cog
RNA binding go/ molecular_function
tRNA processing go/ biological_process
tRNA (guanine-N1-)-methyltransferase activity go/ molecular_function
trmD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_2235
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_2235!

Warning: Synpcc7942_2235 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
1529 4.30e+02 ctT.tc.G.AacttttgacAtC.G
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1530 5.60e+04 cAGaAatcaaAAATT.caaCA
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1531 1.50e+05 CCCtGCaTtG
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1532 5.70e+03 aAaaTTtTtg
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1533 1.30e+04 CtCTGcAA
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1534 2.90e+04 AgtcaAaCaAAggc
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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_2235

Synpcc7942_2235 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
tRNA-(guanine-N1)-methyltransferase cog/ cog
RNA binding go/ molecular_function
tRNA processing go/ biological_process
tRNA (guanine-N1-)-methyltransferase activity go/ molecular_function
trmD tigr/ tigrfam
Module neighborhood information for Synpcc7942_2235

Synpcc7942_2235 has total of 56 gene neighbors in modules 3, 4
Gene neighbors (56)
Gene Common Name Description Module membership
Synpcc7942_0011 hypothetical protein 3, 4
Synpcc7942_0122 EAL 4, 113
Synpcc7942_0152 mraY Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) (IMGterm) 4, 118
Synpcc7942_0171 cysteine synthase (EC:2.5.1.47) 3, 7
Synpcc7942_0173 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase-like 4, 166
Synpcc7942_0357 Inorganic carbon transporter 3, 34
Synpcc7942_0444 hypothetical protein 4, 31
Synpcc7942_0457 hypothetical protein 4, 66
Synpcc7942_0500 hypothetical protein 4, 47
Synpcc7942_0542 lipoic acid synthetase (EC:2.8.1.8) 4, 41
Synpcc7942_0561 hypothetical protein 4, 5
Synpcc7942_0593 hypothetical protein 3, 4
Synpcc7942_0598 Peptidoglycan-binding LysM 3, 31
Synpcc7942_0630 hypothetical protein 1, 3
Synpcc7942_0692 hypothetical protein 4, 179
Synpcc7942_0708 hypothetical protein 3, 186
Synpcc7942_0809 hypothetical protein 3, 46
Synpcc7942_0869 hypothetical protein 4, 65
Synpcc7942_0915 3-dehydroquinate dehydratase (EC 4.2.1.10) (IMGterm) 3, 130
Synpcc7942_0919 hypothetical protein 3, 66
Synpcc7942_0995 conserved hypothetical protein YCF20 3, 88
Synpcc7942_1043 hypothetical protein 3, 31
Synpcc7942_1130 protein serine/threonine phosphatase (IMGterm) 4, 122
Synpcc7942_1188 Ap-4-A phosphorylase II-like protein 4, 100
Synpcc7942_1193 Phospholipid/glycerol acyltransferase 4, 15
Synpcc7942_1214 Glutathione peroxidase (EC:1.11.1.9) 4, 9
Synpcc7942_1260 hypothetical protein 4, 179
Synpcc7942_1311 hypothetical protein 4, 187
Synpcc7942_1338 hypothetical protein 3, 13
Synpcc7942_1375 hypothetical protein 3, 4
Synpcc7942_1439 NADH dehydrogenase subunit M (EC 1.6.5.3) (IMGterm) 4, 66
Synpcc7942_1493 mazG MazG family protein (EC:3.6.1.19) 4, 46
Synpcc7942_1528 conserved hypothetical protein YCF49 3, 4
Synpcc7942_1544 panthotenate metabolism flavoprotein 3, 19
Synpcc7942_1606 Beta-Ig-H3/fasciclin 4, 65
Synpcc7942_1680 Sulphate transport system permease protein 1 (EC:3.6.3.25) 4, 186
Synpcc7942_1681 Thiosulphate-binding protein 3, 186
Synpcc7942_1689 thiosulfate sulfurtransferase (EC 2.8.1.1) (IMGterm) 4, 46
Synpcc7942_1744 hypothetical protein (EC:3.1.2.-) 4, 130
Synpcc7942_1781 molybdopterin synthase subunit MoaD (IMGterm) 3, 125
Synpcc7942_1919 "transcriptional regulator, XRE family (IMGterm)" 3, 61
Synpcc7942_2007 coaD Phosphopantetheine adenylyltransferase (EC 2.7.7.3) (IMGterm) 3, 13
Synpcc7942_2035 hypothetical protein 3, 15
Synpcc7942_2039 hypothetical protein 3, 65
Synpcc7942_2042 hypothetical protein 4, 80
Synpcc7942_2145 hypothetical protein (EC:3.5.1.53) 4, 65
Synpcc7942_2155 hypothetical protein 4, 150
Synpcc7942_2234 NADH dehydrogenase I subunit N (EC:1.6.5.3) 4, 66
Synpcc7942_2235 trmD tRNA (Guanine37-N(1)-) methyltransferase (EC 2.1.1.31) (IMGterm) 3, 4
Synpcc7942_2292 hypothetical protein 3, 4
Synpcc7942_2294 hypothetical protein 3, 13
Synpcc7942_2303 Dihydropteroate synthase (EC 2.5.1.15) (IMGterm) 3, 15
Synpcc7942_2409 Adenylosuccinate synthetase (EC 6.3.4.4) (IMGterm) 3, 16
Synpcc7942_2414 hypothetical protein 3, 124
Synpcc7942_2454 adenine phosphoribosyltransferase (EC 2.4.2.7) (IMGterm) 3, 186
Synpcc7942_2454_2 adenine phosphoribosyltransferase (EC 2.4.2.7) (IMGterm) 3, 31
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_2235
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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