Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4130 to 4179 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2065 ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Divided 214.328 212.561 1.00831
2066 ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Subtracted 207.665 205.948 1.717
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Divided 229.102 231.001 1.00829
2067 adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] 193.226 191.639 1.00828
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Subtracted 207.655 205.939 1.716
2068 fas apoptotic inhibitory molecule. [refseq;acc:nm_018147] Divided 220.8 222.61 1.0082
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Subtracted 207.638 205.923 1.715
2069 dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] Divided 217.555 215.807 1.0081
fidgetin-like 1. [refseq;acc:nm_022116] Subtracted 215.511 213.814 1.697
2070 maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] 218.124 216.433 1.691
rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Divided 223.199 225.008 1.0081
2071 adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] Subtracted 199.928 198.24 1.688
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Divided 217.555 215.807 1.0081
2072 dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507]
ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] Subtracted 199.928 198.24 1.688
2073 adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367]
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Divided 229.267 227.433 1.00806
2074 dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 216.324 214.599 1.00804
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] Subtracted 215.967 214.28 1.687
2075 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Divided 221.703 223.483 1.00803
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Subtracted 215.967 214.28 1.687
2076 dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]
peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] Divided 221.703 223.483 1.00803
2077 iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413]
phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] Subtracted 215.967 214.28 1.687
2078 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 189.987 191.668 1.681
fidgetin-like 1. [refseq;acc:nm_022116] Divided 215.511 213.814 1.00794
2079 phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] 215.967 214.28 1.00787
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Subtracted 215.258 213.579 1.679
2080 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] 189.999 191.677 1.678
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Divided 215.967 214.28 1.00787
2081 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] Subtracted 189.999 191.677 1.678
dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690] Divided 215.967 214.28 1.00787
2082 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] Subtracted 196.808 195.141 1.667
phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] Divided 215.967 214.28 1.00787
2083 serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Subtracted 215.144 213.479 1.665
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Divided 215.258 213.579 1.00786
2084 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] 222.548 224.293 1.00784
ubiquilin 1 isoform 1. [refseq;acc:nm_013438] Subtracted 196.837 195.173 1.664
2085 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] 190.551 192.191 1.64
isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p50213] Divided 222.58 224.32 1.00782
2086 isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:o43837]
limkain beta 2. [refseq;acc:nm_025140] Subtracted 217.723 216.089 1.634
2087 isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553] Divided 222.58 224.32 1.00782
rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701] Subtracted 211.679 210.052 1.627
2088 evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] 211.992 210.369 1.623
maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Divided 218.124 216.433 1.00781
2089 ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] Subtracted 209.994 208.387 1.607
serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Divided 215.144 213.479 1.0078
2090 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Subtracted 214.979 213.39 1.589

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/