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