Organism : Methanococcus maripaludis S2 | Module List :
MMP0970 lig

DNA ligase I, ATP-dependent Dnl1

CircVis
Functional Annotations (12)
Function System
ATP-dependent DNA ligase cog/ cog
DNA binding go/ molecular_function
DNA ligase (ATP) activity go/ molecular_function
ATP binding go/ molecular_function
DNA replication go/ biological_process
DNA repair go/ biological_process
DNA recombination go/ biological_process
DNA replication kegg/ kegg pathway
Base excision repair kegg/ kegg pathway
Nucleotide excision repair kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
dnl1 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0970
(Mouseover regulator name to see its description)

MMP0970 is regulated by 11 influences and regulates 0 modules.
Regulators for MMP0970 lig (11)
Regulator Module Operator
MMP0033 47 tf
MMP0033
MMP0629
47 combiner
MMP0629
MMP1499
47 combiner
MMP0907
MMP1023
47 combiner
MMP1704 47 tf
MMP0168
MMP0907
129 combiner
MMP0637 129 tf
MMP0787
MMP0907
129 combiner
MMP1023
MMP1303
129 combiner
MMP1303
H2
129 combiner
MMP1376
H2
129 combiner

Warning: MMP0970 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
755 3.90e+02 TaA.TTaTccGgaAATTaCc
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756 4.00e+03 CCCCtCC
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911 2.10e+03 tccGCCAC
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912 2.40e+04 CCacACcGTGC
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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 MMP0970

MMP0970 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
ATP-dependent DNA ligase cog/ cog
DNA binding go/ molecular_function
DNA ligase (ATP) activity go/ molecular_function
ATP binding go/ molecular_function
DNA replication go/ biological_process
DNA repair go/ biological_process
DNA recombination go/ biological_process
DNA replication kegg/ kegg pathway
Base excision repair kegg/ kegg pathway
Nucleotide excision repair kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
dnl1 tigr/ tigrfam
Module neighborhood information for MMP0970

MMP0970 has total of 44 gene neighbors in modules 47, 129
Gene neighbors (44)
Gene Common Name Description Module membership
Antisense_13 None 49, 129
MMP0036 tfe transcription initiation factor E subunit alpha 49, 87, 92, 129
MMP0072 hypothetical protein MMP0072 28, 129
MMP0131 L-tyrosine decarboxylase 111, 122, 129, 157
MMP0264 MscMJ mechanosensitive ion channel MscS 129, 143
MMP0265 hypothetical protein MMP0265 28, 129
MMP0291 hydrogenase expression/formation protein-like protein 47, 122
MMP0296 hypothetical protein MMP0296 4, 129
MMP0320 shikimate kinase 47, 141
MMP0415 O-sialoglycoprotein endopeptidase/protein kinase 47, 149
MMP0554 SAM-binding motif-containing protein 129, 140
MMP0580 act anaerobic ribonucleoside-triphosphate reductase activating protein 115, 129
MMP0582 AzlC family protein 47, 68
MMP0681 xanthine/uracil permease family protein 47, 162
MMP0713 iorA2 indolepyruvate oxidoreductase subunit alpha 2 24, 47, 86
MMP0714 iorB2 indolepyruvate oxidoreductase subunit beta 24, 47, 86
MMP0876 cofG FO synthase subunit 1 1, 129
MMP0883 hypothetical protein MMP0883 115, 129
MMP0906 ribonuclease Z 129, 149
MMP0938 cobS cobalamin (5'-phosphate) synthase 47, 122
MMP0941 hypothetical protein MMP0941 129, 149
MMP0970 lig DNA ligase I, ATP-dependent Dnl1 47, 129
MMP1011 gltX glutamyl-tRNA synthetase 25, 129
MMP1024 MCE family-like protein 14, 47, 157
MMP1109 hypothetical protein MMP1109 111, 129
MMP1112 hypothetical protein MMP1112 111, 129, 141, 149
MMP1117 hypothetical protein MMP1117 14, 47, 52, 139
MMP1121 metal-dependent phophohydrolase-like protein 129, 157
MMP1128 ppiB cyclophilin type peptidyl-prolyl cis-trans isomerase 47, 86
MMP1143 hypothetical protein MMP1143 14, 47
MMP1265 glutamyl-tRNA(Gln) amidotransferase subunit E 28, 129
MMP1287 hypothetical protein MMP1287 14, 47, 80
MMP1288 UbiD family decarboxylase 47, 80
MMP1313 fen-1 flap endonuclease-1 47, 52, 141
MMP1334 solute-binding protein/glutamate receptor 41, 129
MMP1348 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase 14, 47
MMP1350 radical SAM domain-containing protein 14, 47, 104
MMP1356 PP-loop domain-containing protein 25, 129, 139, 140, 149
MMP1440 tRNA-modifying protein 129, 137
MMP1467 ehaT hypothetical protein MMP1467 28, 129, 133
MMP1600 ribosomal protein S6 modification protein 104, 129
MMP1630 ABC transporter ATPase 129, 133
MMP1648 hypothetical protein MMP1648 14, 47, 52, 139
Unanno_61 None 111, 129
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 MMP0970
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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