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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Network Comparison Type Gene Rank description Value Type green red network_comparison Interaction Map Filtered
Results: HTML CSV LaTeX Showing element 1 to 50 of 16578 in total
Network Comparison Type  : Divided
Value Type  : Measured
Filtered  : 1
Rank
description
green
red
network_comparison
Interaction Map
1 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 543.5 2399.5 4.4149 Low confidence
rad50-interacting protein 1. [refseq;acc:nm_021930] 2394.5 450.5 5.31521 High confidence
2 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 543.5 2399.5 4.4149 Low confidence
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 2394.5 450.5 5.31521 High confidence
3 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 543.5 2399.5 4.4149 Low confidence
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 698.5 2597.5 3.71868 High confidence
4 hbs1-like. [refseq;acc:nm_006620]
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 543.5 2399.5 4.4149 Low confidence
5 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 339.5 1153.5 3.39764 High confidence
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 2113.5 736.5 2.86965 Low confidence
6 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 339.5 1153.5 3.39764 High confidence
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 2113.5 736.5 2.86965 Low confidence
7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]
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 1153.5 3.39764 High confidence
8 db83 protein. [swissprot;acc:p57088]
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 5058.5 3278 1.54317 Low confidence
9 n33 protein. [swissprot;acc:q13454]
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1281.5 398.5 3.21581 High confidence
10 implantation-associated protein. [refseq;acc:nm_032121] 5058.5 3278 1.54317 Low confidence
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 1281.5 398.5 3.21581 High confidence
11 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 2950.5 1917.64 1.53861 Low confidence
12 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 1281.5 398.5 3.21581 High confidence
gbp protein isoform a. [refseq;acc:nm_017870] 2954.24 1921.96 1.5371 Low confidence
13 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1281.5 398.5 3.21581 High confidence
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 2959.19 1927.68 1.5351 Low confidence
14 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 1281.5 398.5 3.21581 High confidence
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 2998.1 1972.65 1.51983 Low confidence
15 trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] 3007.85 1983.91 1.51612
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 871 2671 3.06659 High confidence
16 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 28492 21185 1.34491 Low confidence
protein x 0004. [refseq;acc:nm_016301] 871 2671 3.06659 High confidence
17 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 1365 460 2.96739
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 28492 21185 1.34491 Low confidence
18 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 7251 5492.04 1.32027
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 1865.5 677.5 2.75351 High confidence
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] 3915.4 3032.56 1.29112 Low confidence
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 1865.5 677.5 2.75351 High confidence
20 protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 9368.87 7256.71 1.29106 Low confidence
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] 3917.88 3035.43 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] 1865.5 677.5 2.75351 High confidence
22 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 3126.88 1.27828 Low 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] 1865.5 677.5 2.75351 High confidence
23 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 32028.5 40899 1.27696 Low confidence
gbp protein isoform a. [refseq;acc:nm_017870] 1894.39 699.76 2.7072 High confidence
24 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 4577.5 5720.25 1.24965 Low confidence
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 2108.52 950.561 2.21818 High confidence
25 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 892.67 1833.01 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] 4691.96 5847.46 1.24627 Low confidence

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/