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 Network Comparison Type red Interaction Map Value Type network_comparison Filtered green
Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
Value Type  : Measured
Rank
description
Network Comparison Type
red
Interaction Map
network_comparison
Filtered
green
1 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Subtracted 85 High confidence 6325 0 6410
Low confidence
carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 40899 8870.5 1 32028.5
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Divided 2399.5 4.4149 543.5
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] Subtracted 41482.5 High confidence 8126 33356.5
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 364 36400000 0 0.00001
Low confidence
rad50-interacting protein 1. [refseq;acc:nm_021930] 450.5 High confidence 5.31521 1 2394.5
2 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Subtracted 21185 Low confidence 7307 28492
cab2. [refseq;acc:nm_033419] Divided 0.00001 High confidence 17400000 0 174
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 2399.5 Low confidence 4.4149 1 543.5
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Subtracted 41482.5 High confidence 8126 33356.5
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 0.00001 Low confidence 8900000 0 89
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted 85 High confidence 6325 6410
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 23818.1 Low confidence 4196.8 19621.3
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided 450.5 High confidence 5.31521 1 2394.5
3 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 2399.5 Low confidence 4.4149 543.5
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Subtracted 41482.5 High confidence 8126 33356.5
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Divided 2597.5 3.71868 698.5
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0.00001 Low confidence 8900000 0 89
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Subtracted 21185 7307 1 28492
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 23818.1 High confidence 4196.8 0 19621.3
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 5106.93 Low confidence 2393.82 7500.75
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Divided 0.00001 High confidence 10900000 109
4 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Subtracted 2082 Low confidence 2274 4356
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 36474.3 7035.1 1 43509.4
cytohesin 4. [swissprot;acc:q9uia0] 41482.5 High confidence 8126 33356.5
hbs1-like. [refseq;acc:nm_006620] Divided 2597.5 3.71868 698.5
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0.00001 Low confidence 8900000 0 89
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 4.4149 1 543.5
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Subtracted 18704 High confidence 3026 0 21730
5 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 41482.5 8126 1 33356.5
histone h4. [swissprot;acc:p02304] 21773.1 2673.2 0 24446.3
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 0.00001 8900000 89
jumonji protein. [swissprot;acc:q92833] Low confidence 1751660 17.5166
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1153.5 High confidence 3.39764 1 339.5
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted 485.286 Low confidence 2254.84 0 2740.13
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Divided 736.5 2.86965 1 2113.5
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Subtracted 36469.3 7034 43503.3
6 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Divided 0.00001 High confidence 8900000 0 89
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 13 Low confidence 1300000 0.00001
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1153.5 High confidence 3.39764 1 339.5
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted 36360.3 Low confidence 7008.5 43368.8
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Divided 736.5 2.86965 2113.5
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Subtracted 44490.5 High confidence 7563 36927.5
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 7592.37 Low confidence 1244.48 0 8836.85
13174.7 High confidence 2430.4 15605.1
7 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 21185 7307 1 28492
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 4660.09 Low confidence 1238.62 0 5898.71

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/