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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Value Type Gene Rank Filtered description Interaction Map Network Comparison Type green red network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 77072 in total
Value Type  : Measured
Rank
Filtered
description
Interaction Map
Network Comparison Type
green
red
network_comparison
1 0 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] High confidence Subtracted 6410 85 6325
Low confidence
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence Divided 0.00001 364 36400000
Low confidence
1 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Subtracted 32028.5 40899 8870.5
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Divided 543.5 2399.5 4.4149
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] High confidence Subtracted 33356.5 41482.5 8126
rad50-interacting protein 1. [refseq;acc:nm_021930] Divided 2394.5 450.5 5.31521
2 0 cab2. [refseq;acc:nm_033419] 174 0.00001 17400000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 89 8900000
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence Subtracted 6410 85 6325
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 19621.3 23818.1 4196.8
1 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 28492 21185 7307
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Divided 543.5 2399.5 4.4149
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence Subtracted 33356.5 41482.5 8126
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided 2394.5 450.5 5.31521
3 0 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 89 0.00001 8900000
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] High confidence Subtracted 19621.3 23818.1 4196.8
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Low confidence 7500.75 5106.93 2393.82
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence Divided 109 0.00001 10900000
1 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 543.5 2399.5 4.4149
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence Subtracted 33356.5 41482.5 8126
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Divided 698.5 2597.5 3.71868
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence Subtracted 28492 21185 7307
4 0 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] 4356 2082 2274
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Divided 89 0.00001 8900000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Subtracted 21730 18704 3026
1 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Low confidence 43509.4 36474.3 7035.1
cytohesin 4. [swissprot;acc:q9uia0] High confidence 33356.5 41482.5 8126
hbs1-like. [refseq;acc:nm_006620] Divided 698.5 2597.5 3.71868
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 543.5 2399.5 4.4149
5 0 histone h4. [swissprot;acc:p02304] High confidence Subtracted 24446.3 21773.1 2673.2
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 89 0.00001 8900000
jumonji protein. [swissprot;acc:q92833] Low confidence 17.5166 1751660
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted 2740.13 485.286 2254.84
1 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] High confidence 33356.5 41482.5 8126
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Divided 339.5 1153.5 3.39764
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 2113.5 736.5 2.86965
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Subtracted 43503.3 36469.3 7034
6 0 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence Divided 89 0.00001 8900000
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] Low confidence 0.00001 13 1300000
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] High confidence Subtracted 15605.1 13174.7 2430.4
Low confidence 8836.85 7592.37 1244.48
1 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence Divided 339.5 1153.5 3.39764
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence Subtracted 43368.8 36360.3 7008.5
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Divided 2113.5 736.5 2.86965
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence Subtracted 36927.5 44490.5 7563
7 0 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Low confidence 5898.71 4660.09 1238.62
sedlin. [swissprot;acc:o14582] High confidence Divided 43 0.00001 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/