Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP1100(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Module neighborhood information for MMP1100
|Gene||Common Name||Description||Module membership|
|Antisense_24||None||5, 49, 90|
|MMP0148||acsA||acetyl-CoA synthetase||17, 124|
|MMP0253||acd||CoA-binding domain-containing protein||95, 124|
|MMP0277||TraB family protein||49, 90|
|MMP0278||putative CBS domain-containing signal transduction protein||19, 90|
|MMP0279||mptG||beta-ribofuranosylaminobenzene 5'-phosphate synthase family protein||49, 90|
|MMP0280||hisI||phosphoribosyl-AMP cyclohydrolase||67, 90|
|MMP0295||thrB||homoserine kinase||64, 90|
|MMP0302||hypothetical protein MMP0302||49, 90|
|MMP0321||hypothetical protein MMP0321||23, 90|
|MMP0344||hypothetical protein MMP0344||19, 90|
|MMP0347||hypothetical protein MMP0347||9, 124|
|MMP0348||GPR1/FUN34/yaaH family protein||17, 124|
|MMP0434||hypothetical protein MMP0434||90, 125|
|MMP0476||hypothetical protein MMP0476||23, 90|
|MMP0477||hypothetical protein MMP0477||23, 90|
|MMP0533||hypothetical protein MMP0533||48, 90|
|MMP0546||AMMECR1 domain-containing protein||124, 159|
|MMP0562||hypothetical protein MMP0562||49, 124|
|MMP0563||hypothetical protein MMP0563||23, 124|
|MMP0613||acetolactate decarboxylase||58, 124|
|MMP0622||ADP-ribosylation/crystallin J1||50, 90|
|MMP0658||MoaA/nifB/pqqE family protein||46, 90|
|MMP0725||putative integral membrane protein||49, 75, 90, 151|
|MMP0728||uvrC||excinuclease ABC subunit C||90, 142|
|MMP0729||uvrA||excinuclease ABC subunit A||46, 90|
|MMP0735||N-6 adenine-specific DNA methylase:N6 adenine-specific DNA methyltransferase, D12 class||44, 90|
|MMP0791||TetR family transcriptional regulator Member||9, 90|
|MMP0977||CooC||CO dehydrogenase maturation factor||17, 124|
|MMP0978||hypothetical protein MMP0978||17, 124|
|MMP0979||hypothetical protein MMP0979||17, 124|
|MMP0980||cdh||acetyl-CoA decarbonylase/synthase complex subunit gamma||17, 124|
|MMP0981||cdhD||acetyl-CoA decarbonylase/synthase complex subunit delta||17, 124|
|MMP0982||hypothetical protein MMP0982||17, 124|
|MMP0983||cdhB||acetyl-CoA decarbonylase/synthase complex subunit beta||17, 124|
|MMP0996||hypothetical protein MMP0996||43, 90, 125|
|MMP0997||blue (type1) copper domain-containing protein||23, 43, 90, 125|
|MMP1100||putative transcriptional regulator||90, 124|
|MMP1164||heavy metal transport/detoxification protein||90, 125, 159|
|MMP1165||heavy metal translocating P-type ATPase||90, 125|
|MMP1166||iron-sulfur flavoprotein||15, 90|
|MMP1167||flavoprotein-like protein||15, 90|
|MMP1224||ABC-type amino acid transport/signal transduction systems periplasmic component-related||23, 90|
|MMP1258||hemB||delta-aminolevulinic acid dehydratase||19, 124|
|MMP1468||hypothetical protein MMP1468||17, 124|
|MMP1553||rdxA||nitroreductase family protein||23, 90, 159|
|MMP1633||hypothetical protein MMP1633||90, 124, 125|
|MMP1634||DsrE family protein||124, 125|
Gene Page Help
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.
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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.
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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.
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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.
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CircVisOur 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.
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