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 Rank Value Type description Network Comparison Type green Filtered Interaction Map network_comparison red
Results: HTML CSV LaTeX Showing element 1 to 50 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
Value Type
description
green
Interaction Map
network_comparison
red
1 Measured lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 543.5 Low confidence 4.4149 2399.5
rad50-interacting protein 1. [refseq;acc:nm_021930] 2394.5 High confidence 5.31521 450.5
Ranked carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 32 Low confidence 2 16
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 24 High confidence 2.4 10
Squared lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 69.9153 Low confidence 19.4914 1362.75
rad50-interacting protein 1. [refseq;acc:nm_021930] 1357.07 High confidence 28.2513 48.0356
Rooted lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 23.3131 Low confidence 2.10117 48.9847
rad50-interacting protein 1. [refseq;acc:nm_021930] 48.9336 High confidence 2.30547 21.225
2 Measured cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 543.5 Low confidence 4.4149 2399.5
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 2394.5 High confidence 5.31521 450.5
Ranked lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 330 Low confidence 1.47982 223
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 28 High confidence 1.86667 15
Squared cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 69.9153 Low confidence 19.4914 1362.75
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1357.07 High confidence 28.2513 48.0356
Rooted cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 23.3131 Low confidence 2.10117 48.9847
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 48.9336 High confidence 2.30547 21.225
3 Measured cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 543.5 Low confidence 4.4149 2399.5
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 698.5 High confidence 3.71868 2597.5
Ranked cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 330 Low confidence 1.47982 223
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 28 High confidence 1.86667 15
Squared cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 69.9153 Low confidence 19.4914 1362.75
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 115.48 High confidence 13.8285 1596.92
Rooted cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 23.3131 Low confidence 2.10117 48.9847
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 26.4292 High confidence 1.92839 50.9657
4 Measured hbs1-like. [refseq;acc:nm_006620] 698.5 3.71868 2597.5
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 543.5 Low confidence 4.4149 2399.5
Ranked cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 330 1.47982 223
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 28 High confidence 1.86667 15
Squared hbs1-like. [refseq;acc:nm_006620] 115.48 13.8285 1596.92
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 69.9153 Low confidence 19.4914 1362.75
Rooted hbs1-like. [refseq;acc:nm_006620] 26.4292 High confidence 1.92839 50.9657
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 23.3131 Low confidence 2.10117 48.9847
5 Measured junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 339.5 High confidence 3.39764 1153.5
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 2113.5 Low confidence 2.86965 736.5
Ranked cytohesin 4. [swissprot;acc:q9uia0] 28 High confidence 1.86667 15
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 330 Low confidence 1.47982 223
Squared junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 27.2805 High confidence 11.544 314.926
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 1057.25 Low confidence 8.23493 128.386
Rooted junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 18.4255 High confidence 1.84327 33.9632
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 45.9728 Low confidence 1.69401 27.1385
6 Measured junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 339.5 High confidence 3.39764 1153.5
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 2113.5 Low confidence 2.86965 736.5
Ranked cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 28 High confidence 1.86667 15
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 240 Low confidence 1.325 318
Squared junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 27.2805 High confidence 11.544 314.926
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 1057.25 Low confidence 8.23493 128.386
Rooted junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 18.4255 High confidence 1.84327 33.9632
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 45.9728 Low confidence 1.69401 27.1385
7 Measured oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 2113.5 2.86965 736.5
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] 339.5 High confidence 3.39764 1153.5

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/