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 51 to 100 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
description
Interaction Map
Filtered
red
green
network_comparison
13 fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] Low confidence 0 8.11997 115.385 14.21
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 1 1927.68 2959.19 1.5351
14 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] High confidence 0 130.512 6.50325 20.0687
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] Low confidence 0.00001 59 5900000
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] High confidence 1 398.5 1281.5 3.21581
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Low confidence 1972.65 2998.1 1.51983
15 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 485.286 2740.13 5.64642
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] High confidence 10 156 15.6
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Low confidence 1 1983.91 3007.85 1.51612
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 2671 871 3.06659
16 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence 21185 28492 1.34491
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] 0 125 704.5 5.636
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] High confidence 1 15 15
protein x 0004. [refseq;acc:nm_016301] 1 2671 871 3.06659
17 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 460 1365 2.96739
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence 21185 28492 1.34491
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 0 859 58 14.8103
ptd016 protein. [refseq;acc:nm_016125] Low confidence 30 158 5.26667
18 60s ribosomal protein l37a. [swissprot;acc:p12751] High confidence 305.45 26.1599 11.6763
camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Low confidence 99 19 5.21053
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 1 5492.04 7251 1.32027
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] High confidence 677.5 1865.5 2.75351
19 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] 0 305.45 26.1599 11.6763
Low confidence 1 3032.56 3915.4 1.29112
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 0 153 662 4.3268
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] High confidence 1 677.5 1865.5 2.75351
20 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Low confidence 0 570 139 4.10072
ero1-like. [refseq;acc:nm_014584] High confidence 82 0.00001 8200000
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 1 677.5 1865.5 2.75351
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Low confidence 7256.71 9368.87 1.29106
21 cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] 3035.43 3917.88 1.29072
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] High confidence 677.5 1865.5 2.75351
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Low confidence 0 111.278 434.911 3.90833
syntaxin 10 (syn10). [swissprot;acc:o60499] High confidence 118.878 17.6611 6.73106
22 carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615] Low confidence 37 0.00001 3700000
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] 1 3126.88 3997.02 1.27828
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] High confidence 677.5 1865.5 2.75351
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 0 60 0.00001 6000000
23 carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] Low confidence 37 3700000
carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 1 40899 32028.5 1.27696
gbp protein isoform a. [refseq;acc:nm_017870] High confidence 699.76 1894.39 2.7072
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 0 0.00001 59 5900000
24 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Low confidence 1 5720.25 4577.5 1.24965
cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] 0 154 493 3.2013
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] High confidence 1 950.561 2108.52 2.21818
ptd016 protein. [refseq;acc:nm_016125] 0 30 158 5.26667
25 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 1 1833.01 892.67 2.0534
histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] Low confidence 5847.46 4691.96 1.24627
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 0 12.6208 39.8063 3.15402
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] High confidence 148 773 5.22297

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/