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 Filtered red Interaction Map green network_comparison
Results: HTML CSV LaTeX Showing element 9586 to 9635 of 12912 in total
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence
Rank
description
Value Type
red
green
network_comparison
2397 importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] Squared 25703.8 27418.6 1.06671
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Ranked 210.157 210.945 1.00375
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Measured 6707.29 6970.07 1.03918
2398 hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Rooted 60.8344 61.7685 1.01535
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Ranked 182.395 183.079 1.00375
r3h domain protein 1. [swissprot;acc:q15032] Squared 26296.9 28047.6 1.06657
2399 homeobox protein otx1. [swissprot;acc:p32242] Measured 5691.1 5913.92 1.03915
karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] Squared 25712.1 27419 1.06639
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Ranked 182.4 183.083 1.00374
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Rooted 60.8344 61.7685 1.01535
2400 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Measured 4368.44 4539.34 1.03912
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Rooted 60.8344 61.7685 1.01535
peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Ranked 182.4 183.083 1.00374
sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Squared 26996.7 28788.6 1.06637
2401 cone-rod homeobox protein. [swissprot;acc:o43186] Measured 5694.04 5916.78 1.03912
oxidation resistance 1. [refseq;acc:nm_181354] Squared 26996.7 28788.6 1.06637
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Rooted 60.8344 61.7685 1.01535
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Ranked 182.4 183.083 1.00374
2402 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] Measured 5078.5 5275.76 1.03884
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Rooted 60.8344 61.7685 1.01535
cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] Ranked 182.4 183.083 1.00374
lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] Squared 26996.7 28788.6 1.06637
2403 40s ribosomal protein s21. [swissprot;acc:p35265] Measured 5078.5 5275.76 1.03884
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Ranked 182.4 183.083 1.00374
dymeclin. [refseq;acc:nm_017653] Squared 26996.7 28788.6 1.06637
mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Rooted 60.8344 61.7685 1.01535
2404 acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] Ranked 193.389 194.105 1.0037
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Measured 5078.5 5275.76 1.03884
sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368] Squared 26996.7 28788.6 1.06637
transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] Rooted 57.6124 58.4763 1.015
2405 hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 60.6732 61.5778 1.01491
lats homolog 1. [refseq;acc:nm_004690] Squared 26996.7 28788.6 1.06637
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Measured 5078.5 5275.76 1.03884
thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] Ranked 221.677 222.489 1.00366
2406 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Measured 5078.5 5275.76 1.03884
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Rooted 58.7808 57.9198 1.01487
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Squared 26996.7 28788.6 1.06637
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Ranked 182.563 183.232 1.00366
2407 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Rooted 58.7808 57.9198 1.01487
nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782] Squared 26996.7 28788.6 1.06637
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Measured 5078.5 5275.76 1.03884
proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] Ranked 214.234 213.456 1.00364
2408 dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125] Squared 26996.7 28788.6 1.06637
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Ranked 194.407 193.706 1.00362
serpin b11. [swissprot;acc:q96p15] Measured 5078.5 5275.76 1.03884
uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Rooted 58.7808 57.9198 1.01487
2409 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760] Ranked 194.407 193.706 1.00362
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Measured 5078.5 5275.76 1.03884

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/