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 Interaction Map description Filtered Value Type Network Comparison Type green network_comparison red
Results: HTML CSV LaTeX Showing element 1 to 50 of 8289 in total
Filtered  : 1
Value Type  : Measured
Network Comparison Type  : Divided
Rank
Interaction Map
description
green
network_comparison
red
1 High confidence rad50-interacting protein 1. [refseq;acc:nm_021930] 2394.5 5.31521 450.5
Low confidence lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 543.5 4.4149 2399.5
2 High confidence rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 2394.5 5.31521 450.5
Low confidence cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 543.5 4.4149 2399.5
3 High confidence homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 698.5 3.71868 2597.5
Low confidence cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 543.5 4.4149 2399.5
4 High confidence hbs1-like. [refseq;acc:nm_006620] 698.5 3.71868 2597.5
Low confidence lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 543.5 4.4149 2399.5
5 High confidence junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 339.5 3.39764 1153.5
Low confidence oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 2113.5 2.86965 736.5
6 High confidence junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 339.5 3.39764 1153.5
Low confidence oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 2113.5 2.86965 736.5
7 High confidence sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 339.5 3.39764 1153.5
Low confidence oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 2113.5 2.86965 736.5
8 High confidence db83 protein. [swissprot;acc:p57088] 339.5 3.39764 1153.5
Low confidence phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 5058.5 1.54317 3278
9 High confidence tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1281.5 3.21581 398.5
Low confidence n33 protein. [swissprot;acc:q13454] 5058.5 1.54317 3278
10 High confidence tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 1281.5 3.21581 398.5
Low confidence implantation-associated protein. [refseq;acc:nm_032121] 5058.5 1.54317 3278
11 High confidence dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 1281.5 3.21581 398.5
Low confidence thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 2950.5 1.53861 1917.64
12 High confidence cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 1281.5 3.21581 398.5
Low confidence gbp protein isoform a. [refseq;acc:nm_017870] 2954.24 1.5371 1921.96
13 High confidence cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1281.5 3.21581 398.5
Low confidence jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 2959.19 1.5351 1927.68
14 High confidence ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 1281.5 3.21581 398.5
Low confidence trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 2998.1 1.51983 1972.65
15 High confidence xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 871 3.06659 2671
Low confidence trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] 3007.85 1.51612 1983.91
16 High confidence protein x 0004. [refseq;acc:nm_016301] 871 3.06659 2671
Low confidence 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 28492 1.34491 21185
17 High confidence dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 1365 2.96739 460
Low confidence mitochondrial solute carrier protein. [refseq;acc:nm_145305] 28492 1.34491 21185
18 High confidence protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 1865.5 2.75351 677.5
Low confidence cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 7251 1.32027 5492.04
19 High confidence microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 1865.5 2.75351 677.5
Low confidence 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] 3915.4 1.29112 3032.56
20 High confidence protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 1865.5 2.75351 677.5
Low confidence retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 9368.87 1.29106 7256.71
21 High confidence ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 1865.5 2.75351 677.5
Low confidence 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] 3917.88 1.29072 3035.43
22 High confidence protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 1865.5 2.75351 677.5
Low confidence 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] 3997.02 1.27828 3126.88
23 High confidence gbp protein isoform a. [refseq;acc:nm_017870] 1894.39 2.7072 699.76
Low confidence carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 32028.5 1.27696 40899
24 High confidence protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 2108.52 2.21818 950.561
Low confidence atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 4577.5 1.24965 5720.25
25 High confidence guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 892.67 2.0534 1833.01
Low confidence 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] 4691.96 1.24627 5847.46

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/