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 description Value Type Network Comparison Type Interaction Map Filtered green network_comparison red
Results: HTML CSV LaTeX Showing element 1 to 50 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
green
network_comparison
red
1 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Divided Low confidence 32 2 16
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Subtracted High confidence 322 107 215
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 330 223
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Divided High confidence 24 2.4 10
2 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Subtracted Low confidence 330 107 223
hbs1-like. [refseq;acc:nm_006620] High confidence 322 215
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Divided Low confidence 330 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] High confidence 28 1.86667 15
3 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 330 1.47982 223
cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Subtracted 107
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Divided High confidence 28 1.86667 15
rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted 232 105 337
4 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Divided Low confidence 330 1.47982 223
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 28 1.86667 15
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Subtracted Low confidence 330 107 223
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 232 105 337
5 cytohesin 4. [swissprot;acc:q9uia0] Divided 28 1.86667 15
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 330 1.47982 223
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Subtracted 240 78 318
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 309 97 212
6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Divided 28 1.86667 15
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Subtracted Low confidence 240 78 318
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Divided 1.325
protein x 0004. [refseq;acc:nm_016301] Subtracted High confidence 309 97 212
7 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Divided 322 1.49767 215
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 240 1.325 318
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Subtracted 78
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 212.554 76.2 288.754
8 hbs1-like. [refseq;acc:nm_006620] Divided 322 1.49767 215
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Subtracted 362 74 288
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Divided Low confidence 240 1.325 318
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Subtracted 247.246 58.226 305.472
9 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided 44 1.31818 58
gbp protein isoform a. [refseq;acc:nm_017870] Subtracted 247.213 58.186 305.399
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence 362 74 288
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Divided 309 1.45755 212
10 jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Subtracted Low confidence 247.169 58.134 305.303
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Divided 44 1.31818 58
protein x 0004. [refseq;acc:nm_016301] High confidence 309 1.45755 212
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] Subtracted 362 74 288
11 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Divided Low confidence 28.4944 1.30966 37.318
db83 protein. [swissprot;acc:p57088] Subtracted High confidence 362 74 288
rad50-interacting protein 1. [refseq;acc:nm_021930] Divided 232 1.45259 337
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Subtracted Low confidence 246.824 57.724 304.548
12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] High confidence 336.233 69.377 266.856
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided 232 1.45259 337
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Subtracted Low confidence 246.737 57.622 304.359
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Divided 28.5242 1.30933 37.3475
13 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Subtracted High confidence 336.233 69.377 266.856
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided Low confidence 29.1831 1.30207 37.9984

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/