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 3730 to 3779 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1865 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Divided 221.639 224.046 1.01086
1866 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Subtracted 210.856 213.147 2.291
translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] Divided 221.725 224.133 1.01086
1867 multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] 203.071 200.89
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Subtracted 210.856 213.147 2.291
1868 60s ribosomal protein l28. [swissprot;acc:p46779] 215.896 213.61 2.286
protein kinase nyd-sp25. [refseq;acc:nm_033516] Divided 207.642 209.895 1.01085
1869 immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Subtracted 218.414 216.131 2.283
lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] Divided 220.107 217.75 1.01082
1870 lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055]
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Subtracted 212.186 214.467 2.281
1871 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] Divided 222.819 225.228 1.01081
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Subtracted 212.186 214.467 2.281
1872 dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Divided 222.819 225.228 1.01081
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Subtracted 212.186 214.467 2.281
1873 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 193.1 190.823 2.277
scratch; scratch 1. [refseq;acc:nm_031309] Divided 210.55 208.305 1.01078
1874 nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Subtracted 193.138 190.861 2.277
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Divided 223.862 226.271 1.01076
1875 nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Subtracted 193.111 190.834 2.277
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Divided 223.862 226.271 1.01076
1876 estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] Subtracted 185.276 187.534 2.258
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Divided 223.862 226.271 1.01076
1877 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 212.186 214.467 1.01075
protein kinase nyd-sp25. [refseq;acc:nm_033516] Subtracted 207.642 209.895 2.253
1878 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Divided 212.186 214.467 1.01075
scratch; scratch 1. [refseq;acc:nm_031309] Subtracted 210.55 208.305 2.245
1879 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 210.592 208.355 2.237
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Divided 212.186 214.467 1.01075
1880 calmegin precursor. [swissprot;acc:o14967] Subtracted 217.48 215.256 2.224
cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] Divided 220.852 223.225 1.01074
1881 calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] Subtracted 217.48 215.256 2.224
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Divided 210.592 208.355 1.01074
1882 60s ribosomal protein l28. [swissprot;acc:p46779] 215.896 213.61 1.0107
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Subtracted 217.48 215.256 2.224
1883 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Divided 240.317 242.881 1.01067
rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799] Subtracted 217.48 215.256 2.224
1884 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 221.607 219.386 2.221
putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Divided 215.081 217.373 1.01066
1885 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] 204.44 206.615 1.01064
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Subtracted 180.609 178.393 2.216
1886 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 215.853 213.639 2.214
arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Divided 204.512 206.682 1.01061
1887 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Subtracted 180.537 178.325 2.212
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Divided 220.896 218.577 1.01061
1888 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] Subtracted 224.264 222.055 2.209
immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Divided 218.414 216.131 1.01056
1889 centaurin gamma 2. [swissprot;acc:q9upq3] Subtracted 220.659 218.452 2.207
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Divided 211.27 209.067 1.01054
1890 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Subtracted 220.659 218.452 2.207

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/