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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Gene Value Type Network Comparison Type Rank green Filtered red Interaction Map description network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 77072 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
green
Filtered
red
Interaction Map
description
network_comparison
1 0.00001 0 364 High confidence mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 36400000
Low confidence
543.5 1 2399.5 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 4.4149
2394.5 450.5 High confidence rad50-interacting protein 1. [refseq;acc:nm_021930] 5.31521
2 89 0 0.00001 Low confidence homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 8900000
174 High confidence cab2. [refseq;acc:nm_033419] 17400000
543.5 1 2399.5 Low confidence cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 4.4149
2394.5 450.5 High confidence rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 5.31521
3 89 0 0.00001 Low confidence homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 8900000
109 High confidence pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 10900000
543.5 1 2399.5 Low confidence cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 4.4149
698.5 2597.5 High confidence homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 3.71868
4 89 0 0.00001 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 8900000
Low confidence homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
543.5 1 2399.5 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 4.4149
698.5 2597.5 High confidence hbs1-like. [refseq;acc:nm_006620] 3.71868
5 17.5166 0 0.00001 Low confidence jumonji protein. [swissprot;acc:q92833] 1751660
89 High confidence homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 8900000
339.5 1 1153.5 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 3.39764
2113.5 736.5 Low confidence oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 2.86965
6 0.00001 0 13 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 1300000
89 0.00001 High confidence homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 8900000
339.5 1 1153.5 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 3.39764
2113.5 736.5 Low confidence oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 2.86965
7 0.00001 0 2.31962 tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] 231962
43 0.00001 High confidence sedlin. [swissprot;acc:o14582] 4300000
339.5 1 1153.5 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
2113.5 736.5 Low confidence oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 2.86965
8 43 0 0.00001 High confidence synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 4300000
339.5 1 1153.5 db83 protein. [swissprot;acc:p57088] 3.39764
5058.5 3278 Low confidence phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 1.54317
6410 0 85 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 75.4118
9 10.6048 383.762 ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 36.1876
1281.5 1 398.5 High confidence tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 3.21581
5058.5 3278 Low confidence n33 protein. [swissprot;acc:q13454] 1.54317
6410 0 85 High confidence ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 75.4118
10 5.56738 199.549 Low confidence serpin b12. [swissprot;acc:q96p63] 35.8425
1281.5 1 398.5 High confidence tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 3.21581
5058.5 3278 Low confidence implantation-associated protein. [refseq;acc:nm_032121] 1.54317
6410 0 85 High confidence lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 75.4118
11 5.56738 199.549 serpin b12. [swissprot;acc:q96p63] 35.8425
5.71669 199.249 Low confidence hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 34.8539
1281.5 1 398.5 High confidence dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 3.21581
2950.5 1917.64 Low confidence thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 1.53861
12 5.71669 0 199.249 High confidence hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 34.8539
58 859 Low confidence mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14.8103
1281.5 1 398.5 High confidence cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 3.21581
2954.24 1921.96 Low confidence gbp protein isoform a. [refseq;acc:nm_017870] 1.5371
13 47 0 1363 High confidence adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 29
115.385 8.11997 Low confidence 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] 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/