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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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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 4151 to 4200 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2076 dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690] Subtracted 215.967 214.28 1.687
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
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] Divided 222.609 224.344 1.00779
2091 adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Subtracted 193.226 191.639 1.587
rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701] Divided 211.679 210.052 1.00775
2092 dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1] Subtracted 223.415 224.989 1.574
evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] Divided 211.992 210.369 1.00772
2093 gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793] Subtracted 226.277 227.851 1.574
ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] Divided 209.994 208.387 1.00771
2094 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 207.321 205.747 1.00765
Subtracted 1.574
2095 lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358] 216.23 217.801 1.571
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Divided 229.266 227.53 1.00763
2096 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] Subtracted 216.36 217.93 1.57
limkain beta 2. [refseq;acc:nm_025140] Divided 217.723 216.089 1.00756
2097 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] 214.979 213.39 1.00745
transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Subtracted 214.666 216.236 1.57
2098 ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792] 219.032 217.47 1.562
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Divided 177.515 178.831 1.00741
2099 ubiquitin-like protein smt3a. [swissprot;acc:p55854] 211.71 213.27 1.00737
Subtracted 1.56
2100 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Divided 1.00737
Subtracted 1.56

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/