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 description Gene Network Comparison Type Interaction Map red network_comparison Value Type Filtered green
Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
Value Type  : Measured
Rank
description
Network Comparison Type
Interaction Map
red
network_comparison
Filtered
green
1 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Subtracted High confidence 85 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 High confidence 41482.5 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] High confidence 450.5 5.31521 1 2394.5
2 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Subtracted Low confidence 21185 7307 28492
cab2. [refseq;acc:nm_033419] Divided High confidence 0.00001 17400000 0 174
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 2399.5 4.4149 1 543.5
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Subtracted High confidence 41482.5 8126 33356.5
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided Low confidence 0.00001 8900000 0 89
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted High confidence 85 6325 6410
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 23818.1 4196.8 19621.3
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided High confidence 450.5 5.31521 1 2394.5
3 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 2399.5 4.4149 543.5
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Subtracted High confidence 41482.5 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] Low confidence 0.00001 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] High confidence 23818.1 4196.8 0 19621.3
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Low confidence 5106.93 2393.82 7500.75
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Divided High confidence 0.00001 10900000 109
4 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Subtracted Low confidence 2082 2274 4356
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 36474.3 7035.1 1 43509.4
cytohesin 4. [swissprot;acc:q9uia0] High confidence 41482.5 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] Low confidence 0.00001 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] Low confidence 2399.5 4.4149 1 543.5
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Subtracted High confidence 18704 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] High confidence 1153.5 3.39764 1 339.5
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted Low confidence 485.286 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 High confidence 0.00001 8900000 0 89
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] Low confidence 13 1300000 0.00001
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence 1153.5 3.39764 1 339.5
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted Low confidence 36360.3 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 High confidence 44490.5 7563 36927.5
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 13174.7 2430.4 0 15605.1
Low confidence 7592.37 1244.48 8836.85
7 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] High confidence 21185 7307 1 28492
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Low confidence 4660.09 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/