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 5636 to 5685 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1409 trap/mediator complex component trap25. [refseq;acc:nm_080651] Ranked 206.102 210.42 1.02095
1410 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Measured 6274.62 6760.78 1.07748
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Rooted 65.3456 67.9119 1.03927
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Squared 17102.5 19171.7 1.12099
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] Ranked 206.1 210.417 1.02095
1411 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] Measured 5812.02 6262.07 1.07743
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Rooted 65.3456 67.9119 1.03927
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Squared 8107.35 9087.76 1.12093
serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013] Ranked 206.102 210.42 1.02095
1412 heat shock cognate 71 kda protein. [swissprot;acc:p11142] Rooted 65.3456 67.9119 1.03927
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Measured 5813.84 6263.92 1.07742
polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] Ranked 206.102 210.42 1.02095
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Squared 22981.1 25758.4 1.12085
1413 acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] Ranked 206.102 210.42 1.02095
histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Measured 5813.88 6263.97 1.07742
homolog of yeast maf1. [refseq;acc:nm_032272] Rooted 65 67.552 1.03926
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] Squared 22981.1 25758.4 1.12085
1414 histone deacetylase 4 (hd4). [swissprot;acc:p56524] Measured 5813.88 6263.96 1.07741
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Ranked 206.102 210.42 1.02095
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Rooted 65 67.552 1.03926
uridine kinase-like 1. [swissprot;acc:q9nwz5] Squared 24302 27238.6 1.12084
1415 14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] Measured 5815.33 6265.44 1.0774
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Squared 26893.1 30139.8 1.12073
stromal interaction molecule 2 precursor. [swissprot;acc:q9p246] Ranked 206.102 210.42 1.02095
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Rooted 52.359 50.3808 1.03926
1416 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Squared 26893.1 30139.8 1.12073
lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] Rooted 61.2971 63.7036 1.03926
serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286] Ranked 206.102 210.42 1.02095
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Measured 6123.75 6597.71 1.0774
1417 carboxypeptidase a5. [refseq;acc:nm_080385] Ranked 203.979 208.229 1.02084
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Squared 26893.1 30139.8 1.12073
isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p50213] Measured 5360.39 5775.24 1.07739
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Rooted 65 67.552 1.03926
1418 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Ranked 203.979 208.229 1.02084
homeobox protein barh-like 1. [swissprot;acc:q9hbu1] Rooted 52.359 50.3808 1.03926
isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:o43837] Measured 5360.39 5775.24 1.07739
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Squared 26893.1 30139.8 1.12073
1419 isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553] Measured 5360.39 5775.24 1.07739
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Ranked 203.979 208.229 1.02084
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Rooted 52.359 50.3808 1.03926
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Squared 26893.1 30139.8 1.12073
1420 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Ranked 203.979 208.229 1.02084
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Squared 16038 17973.3 1.12067
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] Rooted 52.359 50.3808 1.03926
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Measured 5658.51 6096.21 1.07735
1421 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] Ranked 207.076 211.391 1.02084
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Measured 5628.53 6063.61 1.0773
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Squared 27545 30868 1.12064
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Rooted 65 67.552 1.03926
1422 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Ranked 203.979 208.229 1.02084

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/