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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Gene Value Type Network Comparison Type Rank green description Interaction Map network_comparison Filtered red
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 7460 in total
Value Type  : Ranked
Network Comparison Type  : Subtracted
Interaction Map  : High confidence
Filtered  : 1
Rank
green
description
network_comparison
red
2176 220.108 phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 1.401 221.509
2177 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
2178 beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429]
2179 fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413]
2180 retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329]
2181 indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050]
2182 209.563 peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] 1.398 210.961
2183 heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652]
2184 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]
2185 heat shock cognate 71 kda protein. [swissprot;acc:p11142]
2186 225.005 seven in absentia homolog 1. [refseq;acc:nm_003031] 1.397 223.608
2187 207.796 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 1.395 206.401
2188 210.318 suppressor of var1, 3-like 1. [refseq;acc:nm_003171] 211.713
2189 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
2190 glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840]
2191 glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841]
2192 212.254 p47 protein isoform a. [refseq;acc:nm_016143] 1.388 213.642
2193 219.336 cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] 1.381 217.955
2194 cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281]
2195 214.19 transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072] 215.571
2196 219.336 destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] 217.955
2197 ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890]
2198 208.162 protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] 1.378 209.54
2199 224.337 protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 222.959
2200 224.343 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 222.965
2201 208.162 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] 209.54
2202 zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]
2203 224.337 bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 222.959
2204 224.336 testis-specific bromodomain protein. [refseq;acc:nm_001726] 222.958
2205 208.162 hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507] 209.54
2206 hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282]
2207 224.337 nag14 protein. [refseq;acc:nm_022143] 222.959
2208 208.162 prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] 209.54
2209 homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786]
2210 rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853]
2211 224.338 bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 222.96
2212 208.162 prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] 209.54
2213 224.943 mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] 1.363 223.58
2214 198.71 vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] 1.353 200.063
2215 214.194 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 215.547
2216 198.71 vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] 200.063
2217 vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379]
2218 cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]
2219 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3]
2220 vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836]
2221 211.475 dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] 1.348 210.127
2222 213.153 nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 1.343 211.81
2223 220.377 kinesin-like protein kif3c. [swissprot;acc:o14782] 1.332 219.045
2224 220.371 kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] 1.324 219.047
2225 224.869 seven in absentia homolog 2. [refseq;acc:nm_005067] 1.323 223.546

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/