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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Value Type Gene Network Comparison Type Filtered Rank green description network_comparison Interaction Map red
Results: HTML CSV LaTeX Showing element 1 to 50 of 66312 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
green
description
network_comparison
Interaction Map
red
1 543.5 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 4.4149 Low confidence 2399.5
2394.5 rad50-interacting protein 1. [refseq;acc:nm_021930] 5.31521 High confidence 450.5
2 543.5 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 4.4149 Low confidence 2399.5
2394.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 5.31521 High confidence 450.5
3 543.5 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 4.4149 Low confidence 2399.5
698.5 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 3.71868 High confidence 2597.5
4 543.5 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 4.4149 Low confidence 2399.5
698.5 hbs1-like. [refseq;acc:nm_006620] 3.71868 High confidence 2597.5
5 339.5 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 3.39764 1153.5
2113.5 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 2.86965 Low confidence 736.5
6 339.5 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 3.39764 High confidence 1153.5
2113.5 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 2.86965 Low confidence 736.5
7 339.5 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] 3.39764 High confidence 1153.5
2113.5 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 2.86965 Low confidence 736.5
8 339.5 db83 protein. [swissprot;acc:p57088] 3.39764 High confidence 1153.5
5058.5 phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 1.54317 Low confidence 3278
9 1281.5 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 3.21581 High confidence 398.5
5058.5 n33 protein. [swissprot;acc:q13454] 1.54317 Low confidence 3278
10 1281.5 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 3.21581 High confidence 398.5
5058.5 implantation-associated protein. [refseq;acc:nm_032121] 1.54317 Low confidence 3278
11 1281.5 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 3.21581 High confidence 398.5
2950.5 thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 1.53861 Low confidence 1917.64
12 1281.5 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 3.21581 High confidence 398.5
2954.24 gbp protein isoform a. [refseq;acc:nm_017870] 1.5371 Low confidence 1921.96
13 1281.5 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 3.21581 High confidence 398.5
2959.19 jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 1.5351 Low confidence 1927.68
14 1281.5 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 3.21581 High confidence 398.5
2998.1 trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 1.51983 Low confidence 1972.65
15 871 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 3.06659 High confidence 2671
3007.85 trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] 1.51612 Low confidence 1983.91
16 871 protein x 0004. [refseq;acc:nm_016301] 3.06659 High confidence 2671
28492 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1.34491 Low confidence 21185
17 1365 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 2.96739 High confidence 460
28492 mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1.34491 Low confidence 21185
18 1865.5 protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 2.75351 High confidence 677.5
7251 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 1.32027 Low confidence 5492.04
19 1865.5 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 2.75351 High confidence 677.5
3915.4 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] 1.29112 Low confidence 3032.56
20 1865.5 protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 2.75351 High confidence 677.5
9368.87 retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 1.29106 Low confidence 7256.71
21 1865.5 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 2.75351 High confidence 677.5
3917.88 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] 1.29072 Low confidence 3035.43
22 1865.5 protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 2.75351 High confidence 677.5
3997.02 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] 1.27828 Low confidence 3126.88
23 1894.39 gbp protein isoform a. [refseq;acc:nm_017870] 2.7072 High confidence 699.76
32028.5 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 1.27696 Low confidence 40899
24 2108.52 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 2.21818 High confidence 950.561
4577.5 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 1.24965 Low confidence 5720.25
25 892.67 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 2.0534 High confidence 1833.01
4691.96 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] 1.24627 Low confidence 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/