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 Network Comparison Type Filtered description green Interaction Map red network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Network Comparison Type
description
green
Interaction Map
red
network_comparison
1 Divided carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 32 Low confidence 16 2
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 24 High confidence 10 2.4
Subtracted homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 322 215 107
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 330 Low confidence 223
2 Divided 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
Subtracted cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 330 Low confidence 223 107
hbs1-like. [refseq;acc:nm_006620] 322 High confidence 215
3 Divided 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
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 28 High confidence 15 1.86667
Subtracted cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 330 Low confidence 223 107
rad50-interacting protein 1. [refseq;acc:nm_021930] 232 High confidence 337 105
4 Divided cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 330 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
Subtracted lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 330 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 Divided cytohesin 4. [swissprot;acc:q9uia0] 28 15 1.86667
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 330 Low confidence 223 1.47982
Subtracted oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 240 318 78
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 309 High confidence 212 97
6 Divided cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 28 15 1.86667
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 240 Low confidence 318 1.325
Subtracted oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 78
protein x 0004. [refseq;acc:nm_016301] 309 High confidence 212 97
7 Divided homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 322 215 1.49767
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 240 Low confidence 318 1.325
Subtracted oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 78
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 212.554 High confidence 288.754 76.2
8 Divided hbs1-like. [refseq;acc:nm_006620] 322 215 1.49767
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 240 Low confidence 318 1.325
Subtracted junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 362 High confidence 288 74
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 247.246 Low confidence 305.472 58.226
9 Divided 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 44 58 1.31818
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 309 High confidence 212 1.45755
Subtracted gbp protein isoform a. [refseq;acc:nm_017870] 247.213 Low confidence 305.399 58.186
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 362 High confidence 288 74
10 Divided mitochondrial solute carrier protein. [refseq;acc:nm_145305] 44 Low confidence 58 1.31818
protein x 0004. [refseq;acc:nm_016301] 309 High confidence 212 1.45755
Subtracted jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 247.169 Low confidence 305.303 58.134
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 High confidence 288 74
11 Divided bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 28.4944 Low confidence 37.318 1.30966
rad50-interacting protein 1. [refseq;acc:nm_021930] 232 High confidence 337 1.45259
Subtracted db83 protein. [swissprot;acc:p57088] 362 288 74
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 246.824 Low confidence 304.548 57.724
12 Divided rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 232 High confidence 337 1.45259
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] 28.5242 Low confidence 37.3475 1.30933
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 336.233 High confidence 266.856 69.377
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] 246.737 Low confidence 304.359 57.622
13 Divided nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 29.1831 37.9984 1.30207
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 212.554 High confidence 288.754 1.3585

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/