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 2991 to 3040 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1496 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] High confidence 229.459 225.237 1.01874
vav proto-oncogene. [swissprot;acc:p15498] Low confidence 200.208 196.012 1.02141
1497 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] High confidence 224.476 220.363 1.01866
leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] Low confidence 197.941 193.791 1.02141
1498 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 189.066 185.103
neurotrimin precursor (hnt). [swissprot;acc:q9p121] High confidence 224.022 219.924 1.01863
1499 importin 4. [refseq;acc:nm_024658] Low confidence 201.224 197.007 1.02141
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] High confidence 224.509 220.411 1.01859
1500 cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] 213.398 209.52 1.01851
glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] Low confidence 200.875 196.667 1.0214
1501 kinesin family member c3. [refseq;acc:nm_005550] High confidence 214.727 210.838 1.01845
mitogen-activated protein kinase 7 (ec 2.7.1.37) (extracellular signal-regulated kinase 5) (erk-5) (erk4) (bmk1 kinase). [swissprot;acc:q13164] Low confidence 200.507 196.307 1.0214
1502 swi/snf-related matrix-associated actin-dependent regulator of chromatin a3; snf2-like 3; helicase-like transcription factor; dna-binding protein/plasminogen activator inhibitor-1 regulator; sucrose nonfermenting-like 3. [refseq;acc:nm_003071] 202.287 198.05 1.02139
uridine kinase-like 1. [swissprot;acc:q9nwz5] High confidence 218.084 214.149 1.01838
1503 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 242.181 237.834 1.01828
vav-3 protein. [swissprot;acc:q9ukw4] Low confidence 200.237 196.045 1.02138
1504 epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] 192.267 188.242
m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] High confidence 259.439 254.797 1.01822
1505 glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] Low confidence 202.722 198.48 1.02137
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] High confidence 216.158 212.316 1.0181
1506 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 212.103 208.339 1.01807
ras-related protein rab-8b. [swissprot;acc:q92930] Low confidence 200.685 196.487 1.02137
1507 vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] 198.931 194.769
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] High confidence 213.274 209.5 1.01801
1508 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Low confidence 203.663 199.402 1.02137
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] High confidence 213.274 209.5 1.01801
1509 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 225.148 221.177 1.01795
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Low confidence 204.422 200.147 1.02136
1510 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] High confidence 225.148 221.177 1.01795
peroxiredoxin 1 (ec 1.11.1.-) (thioredoxin peroxidase 2) (thioredoxin- dependent peroxide reductase 2) (proliferation-associated protein pag) (natural killer cell enhancing factor a) (nkef-a). [swissprot;acc:q06830] Low confidence 200.965 196.762 1.02136
1511 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] High confidence 213.268 209.509 1.01794
long-chain-fatty-acid--coa ligase 2 (ec 6.2.1.3) (long-chain acyl-coa synthetase 2) (lacs 2). [swissprot;acc:p33121] Low confidence 204.294 200.024 1.02135
1512 peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] 201.123 196.918
surfeit locus protein 1. [swissprot;acc:q15526] High confidence 213.268 209.509 1.01794
1513 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]
peroxiredoxin 2 (ec 1.11.1.-) (thioredoxin peroxidase 1) (thioredoxin- dependent peroxide reductase 1) (thiol-specific antioxidant protein) (tsa) (prp) (natural killer cell enhancing factor b) (nkef-b). [swissprot;acc:p32119] Low confidence 200.934 196.735 1.02134
1514 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] 195.292 191.212
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] High confidence 213.268 209.509 1.01794
1515 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 213.267 209.511 1.01793
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Low confidence 202.972 198.731 1.02134
1516 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] High confidence 213.267 209.511 1.01793
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Low confidence 198.978 194.82 1.02134
1517 seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] High confidence 213.267 209.511 1.01793
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Low confidence 193.118 189.083 1.02134
1518 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] 200.093 195.912
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] High confidence 213.259 209.524 1.01783
1519 cone-rod homeobox protein. [swissprot;acc:o43186] 244.331 240.061 1.01779
long-chain-fatty-acid--coa ligase 5 (ec 6.2.1.3) (long-chain acyl-coa synthetase 5) (lacs 5). [swissprot;acc:q9ulc5] Low confidence 204.295 200.027 1.02134
1520 homeobox protein otx1. [swissprot;acc:p32242] High confidence 244.367 240.098 1.01778
ras-related protein rab-8 (rab-8a) (oncogene c-mel). [swissprot;acc:p24407] Low confidence 200.683 196.493 1.02132

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/