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

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/