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 Rank Filtered description Network Comparison Type network_comparison Interaction Map green red
Results: HTML CSV LaTeX Showing element 1 to 50 of 14920 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
Filtered
description
network_comparison
green
red
1 0 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 36400000 0.00001 364
1 rad50-interacting protein 1. [refseq;acc:nm_021930] 5.31521 2394.5 450.5
2 0 cab2. [refseq;acc:nm_033419] 17400000 174 0.00001
1 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 5.31521 2394.5 450.5
3 0 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 10900000 109 0.00001
1 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 3.71868 698.5 2597.5
4 0 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 8900000 89 0.00001
1 hbs1-like. [refseq;acc:nm_006620] 3.71868 698.5 2597.5
5 0 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 8900000 89 0.00001
1 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 3.39764 339.5 1153.5
6 0 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 8900000 89 0.00001
1 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 3.39764 339.5 1153.5
7 0 sedlin. [swissprot;acc:o14582] 4300000 43 0.00001
1 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 339.5 1153.5
8 0 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 4300000 43 0.00001
1 db83 protein. [swissprot;acc:p57088] 3.39764 339.5 1153.5
9 0 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 75.4118 6410 85
1 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 3.21581 1281.5 398.5
10 0 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 75.4118 6410 85
1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 3.21581 1281.5 398.5
11 0 serpin b12. [swissprot;acc:q96p63] 35.8425 5.56738 199.549
1 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 3.21581 1281.5 398.5
12 0 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 34.8539 5.71669 199.249
1 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 3.21581 1281.5 398.5
13 0 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 29 47 1363
1 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 3.21581 1281.5 398.5
14 0 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 20.0687 6.50325 130.512
1 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 3.21581 1281.5 398.5
15 0 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] 15.6 156 10
1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 3.06659 871 2671
16 0 protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 15 15 1
1 protein x 0004. [refseq;acc:nm_016301] 3.06659 871 2671
17 0 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14.8103 58 859
1 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 2.96739 1365 460
18 0 60s ribosomal protein l37a. [swissprot;acc:p12751] 11.6763 26.1599 305.45
1 protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 2.75351 1865.5 677.5
19 0 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] 11.6763 26.1599 305.45
1 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 2.75351 1865.5 677.5
20 0 ero1-like. [refseq;acc:nm_014584] 8200000 0.00001 82
1 protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 2.75351 1865.5 677.5
21 0 syntaxin 10 (syn10). [swissprot;acc:o60499] 6.73106 17.6611 118.878
1 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 1865.5 677.5
22 0 similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 6000000 0.00001 60
1 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 1865.5 677.5
23 0 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] 5900000 59 0.00001
1 gbp protein isoform a. [refseq;acc:nm_017870] 2.7072 1894.39 699.76
24 0 ptd016 protein. [refseq;acc:nm_016125] 5.26667 158 30
1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 2.21818 2108.52 950.561
25 0 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 5.22297 773 148
1 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 2.0534 892.67 1833.01

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/