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