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 Network Comparison Type description red Filtered Interaction Map network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 38536 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
green
description
red
Filtered
Interaction Map
network_comparison
1 0.00001 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 364 0 High confidence 36400000
Low confidence
543.5 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 2399.5 1 4.4149
2394.5 rad50-interacting protein 1. [refseq;acc:nm_021930] 450.5 High confidence 5.31521
2 89 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0.00001 0 Low confidence 8900000
174 cab2. [refseq;acc:nm_033419] High confidence 17400000
543.5 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 2399.5 1 Low confidence 4.4149
2394.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 450.5 High confidence 5.31521
3 89 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0.00001 0 Low confidence 8900000
109 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 10900000
543.5 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 2399.5 1 Low confidence 4.4149
698.5 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 2597.5 High confidence 3.71868
4 89 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0.00001 0 Low confidence 8900000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
543.5 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 2399.5 1 Low confidence 4.4149
698.5 hbs1-like. [refseq;acc:nm_006620] 2597.5 High confidence 3.71868
5 17.5166 jumonji protein. [swissprot;acc:q92833] 0.00001 0 Low confidence 1751660
89 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 8900000
339.5 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1153.5 1 3.39764
2113.5 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 736.5 Low confidence 2.86965
6 0.00001 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 13 0 1300000
89 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0.00001 High confidence 8900000
339.5 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1153.5 1 3.39764
2113.5 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 736.5 Low confidence 2.86965
7 0.00001 tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] 2.31962 0 231962
43 sedlin. [swissprot;acc:o14582] 0.00001 High confidence 4300000
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] 1153.5 1 3.39764
2113.5 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 736.5 Low confidence 2.86965
8 43 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 0.00001 0 High confidence 4300000
339.5 db83 protein. [swissprot;acc:p57088] 1153.5 1 3.39764
5058.5 phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 3278 Low confidence 1.54317
6410 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 85 0 75.4118
9 10.6048 ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 383.762 36.1876
1281.5 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 398.5 1 High confidence 3.21581
5058.5 n33 protein. [swissprot;acc:q13454] 3278 Low confidence 1.54317
6410 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 85 0 High confidence 75.4118
10 5.56738 serpin b12. [swissprot;acc:q96p63] 199.549 Low confidence 35.8425
1281.5 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 398.5 1 High confidence 3.21581
5058.5 implantation-associated protein. [refseq;acc:nm_032121] 3278 Low confidence 1.54317
6410 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 85 0 High confidence 75.4118
11 5.56738 serpin b12. [swissprot;acc:q96p63] 199.549 35.8425
5.71669 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 199.249 Low confidence 34.8539
1281.5 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 398.5 1 High confidence 3.21581
2950.5 thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 1917.64 Low confidence 1.53861
12 5.71669 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 199.249 0 High confidence 34.8539
58 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 859 Low confidence 14.8103
1281.5 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 398.5 1 High confidence 3.21581
2954.24 gbp protein isoform a. [refseq;acc:nm_017870] 1921.96 Low confidence 1.5371
13 47 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 1363 0 High confidence 29
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] 8.11997 Low confidence 14.21

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/