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 Network Comparison Type description red Interaction Map Value Type Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
Value Type  : Measured
Rank
Network Comparison Type
description
red
Interaction Map
Filtered
green
network_comparison
1 Divided lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 2399.5 Low confidence 1 543.5 4.4149
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 364 High confidence 0 0.00001 36400000
Low confidence
rad50-interacting protein 1. [refseq;acc:nm_021930] 450.5 High confidence 1 2394.5 5.31521
Subtracted ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 85 0 6410 6325
Low confidence
carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 40899 1 32028.5 8870.5
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] 41482.5 High confidence 33356.5 8126
2 Divided cab2. [refseq;acc:nm_033419] 0.00001 0 174 17400000
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 2399.5 Low confidence 1 543.5 4.4149
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0.00001 0 89 8900000
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 450.5 High confidence 1 2394.5 5.31521
Subtracted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 21185 Low confidence 28492 7307
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 41482.5 High confidence 33356.5 8126
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 85 0 6410 6325
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 23818.1 Low confidence 19621.3 4196.8
3 Divided cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 2399.5 1 543.5 4.4149
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 2597.5 High confidence 698.5 3.71868
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0.00001 Low confidence 0 89 8900000
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 109 10900000
Subtracted cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 41482.5 1 33356.5 8126
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 21185 Low confidence 28492 7307
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 23818.1 High confidence 0 19621.3 4196.8
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 5106.93 Low confidence 7500.75 2393.82
4 Divided hbs1-like. [refseq;acc:nm_006620] 2597.5 High confidence 1 698.5 3.71868
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0.00001 Low confidence 0 89 8900000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 2399.5 Low confidence 1 543.5 4.4149
Subtracted anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] 2082 0 4356 2274
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 36474.3 1 43509.4 7035.1
cytohesin 4. [swissprot;acc:q9uia0] 41482.5 High confidence 33356.5 8126
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 18704 0 21730 3026
5 Divided homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0.00001 89 8900000
jumonji protein. [swissprot;acc:q92833] Low confidence 17.5166 1751660
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1153.5 High confidence 1 339.5 3.39764
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 736.5 Low confidence 2113.5 2.86965
Subtracted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 41482.5 High confidence 33356.5 8126
histone h4. [swissprot;acc:p02304] 21773.1 0 24446.3 2673.2
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 485.286 Low confidence 2740.13 2254.84
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] 36469.3 1 43503.3 7034
6 Divided homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0.00001 High confidence 0 89 8900000
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 13 Low confidence 0.00001 1300000
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1153.5 High confidence 1 339.5 3.39764
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 736.5 Low confidence 2113.5 2.86965
Subtracted nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 36360.3 43368.8 7008.5
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 44490.5 High confidence 36927.5 7563
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 7592.37 Low confidence 0 8836.85 1244.48
13174.7 High confidence 15605.1 2430.4
7 Divided oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 736.5 Low confidence 1 2113.5 2.86965
sedlin. [swissprot;acc:o14582] 0.00001 High confidence 0 43 4300000

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/