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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Gene Value Type Rank green Filtered description Network Comparison Type Interaction Map network_comparison red
Results: HTML CSV LaTeX Showing element 1 to 50 of 38536 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
green
Filtered
description
Interaction Map
network_comparison
red
1 0.00001 0 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 36400000 364
Low confidence
543.5 1 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 4.4149 2399.5
2394.5 rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 5.31521 450.5
2 89 0 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 8900000 0.00001
174 cab2. [refseq;acc:nm_033419] High confidence 17400000
543.5 1 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 4.4149 2399.5
2394.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 5.31521 450.5
3 89 0 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 8900000 0.00001
109 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 10900000
543.5 1 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 4.4149 2399.5
698.5 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] High confidence 3.71868 2597.5
4 89 0 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 8900000 0.00001
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
543.5 1 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 4.4149 2399.5
698.5 hbs1-like. [refseq;acc:nm_006620] High confidence 3.71868 2597.5
5 17.5166 0 jumonji protein. [swissprot;acc:q92833] Low confidence 1751660 0.00001
89 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 8900000
339.5 1 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] Low confidence 2.86965 736.5
6 0.00001 0 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 1300000 13
89 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 8900000 0.00001
339.5 1 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 3.39764 1153.5
2113.5 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 2.86965 736.5
7 0.00001 0 tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] 231962 2.31962
43 sedlin. [swissprot;acc:o14582] High confidence 4300000 0.00001
339.5 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 1153.5
2113.5 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence 2.86965 736.5
8 43 0 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] High confidence 4300000 0.00001
339.5 1 db83 protein. [swissprot;acc:p57088] 3.39764 1153.5
5058.5 phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence 1.54317 3278
6410 0 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 75.4118 85
9 10.6048 ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 36.1876 383.762
1281.5 1 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] High confidence 3.21581 398.5
5058.5 n33 protein. [swissprot;acc:q13454] Low confidence 1.54317 3278
6410 0 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] High confidence 75.4118 85
10 5.56738 serpin b12. [swissprot;acc:q96p63] Low confidence 35.8425 199.549
1281.5 1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence 3.21581 398.5
5058.5 implantation-associated protein. [refseq;acc:nm_032121] Low confidence 1.54317 3278
6410 0 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence 75.4118 85
11 5.56738 serpin b12. [swissprot;acc:q96p63] 35.8425 199.549
5.71669 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Low confidence 34.8539 199.249
1281.5 1 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] High confidence 3.21581 398.5
2950.5 thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Low confidence 1.53861 1917.64
12 5.71669 0 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] High confidence 34.8539 199.249
58 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Low confidence 14.8103 859
1281.5 1 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] High confidence 3.21581 398.5
2954.24 gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 1.5371 1921.96
13 47 0 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] High confidence 29 1363
115.385 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 14.21 8.11997

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/