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 Filtered Network Comparison Type Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 9586 to 9635 of 12912 in total
Filtered  : 1
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
red
network_comparison
green
2397 importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] Squared 25703.8 1.06671 27418.6
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Ranked 210.157 1.00375 210.945
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Measured 6707.29 1.03918 6970.07
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 1.01535 61.7685
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Ranked 182.395 1.00375 183.079
r3h domain protein 1. [swissprot;acc:q15032] Squared 26296.9 1.06657 28047.6
2399 homeobox protein otx1. [swissprot;acc:p32242] Measured 5691.1 1.03915 5913.92
karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] Squared 25712.1 1.06639 27419
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Ranked 182.4 1.00374 183.083
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Rooted 60.8344 1.01535 61.7685
2400 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Measured 4368.44 1.03912 4539.34
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Rooted 60.8344 1.01535 61.7685
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 1.00374 183.083
sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Squared 26996.7 1.06637 28788.6
2401 cone-rod homeobox protein. [swissprot;acc:o43186] Measured 5694.04 1.03912 5916.78
oxidation resistance 1. [refseq;acc:nm_181354] Squared 26996.7 1.06637 28788.6
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Rooted 60.8344 1.01535 61.7685
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Ranked 182.4 1.00374 183.083
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 1.03884 5275.76
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Rooted 60.8344 1.01535 61.7685
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 1.00374 183.083
lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] Squared 26996.7 1.06637 28788.6
2403 40s ribosomal protein s21. [swissprot;acc:p35265] Measured 5078.5 1.03884 5275.76
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Ranked 182.4 1.00374 183.083
dymeclin. [refseq;acc:nm_017653] Squared 26996.7 1.06637 28788.6
mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Rooted 60.8344 1.01535 61.7685
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 1.0037 194.105
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Measured 5078.5 1.03884 5275.76
sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368] Squared 26996.7 1.06637 28788.6
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 1.015 58.4763
2405 hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 60.6732 1.01491 61.5778
lats homolog 1. [refseq;acc:nm_004690] Squared 26996.7 1.06637 28788.6
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Measured 5078.5 1.03884 5275.76
thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] Ranked 221.677 1.00366 222.489
2406 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Measured 5078.5 1.03884 5275.76
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Rooted 58.7808 1.01487 57.9198
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Squared 26996.7 1.06637 28788.6
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Ranked 182.563 1.00366 183.232
2407 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Rooted 58.7808 1.01487 57.9198
nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782] Squared 26996.7 1.06637 28788.6
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Measured 5078.5 1.03884 5275.76
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 1.00364 213.456
2408 dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125] Squared 26996.7 1.06637 28788.6
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Ranked 194.407 1.00362 193.706
serpin b11. [swissprot;acc:q96p15] Measured 5078.5 1.03884 5275.76
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 1.01487 57.9198
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 1.00362 193.706
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Measured 5078.5 1.03884 5275.76

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/