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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank Network Comparison Type red description 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
red
description
Interaction Map
Filtered
green
network_comparison
1 Divided 364 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 0 0.00001 36400000
Low confidence
450.5 rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 1 2394.5 5.31521
2399.5 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 543.5 4.4149
Subtracted 85 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] High confidence 0 6410 6325
Low confidence
40899 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 1 32028.5 8870.5
41482.5 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] High confidence 33356.5 8126
2 Divided 0.00001 cab2. [refseq;acc:nm_033419] 0 174 17400000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 89 8900000
450.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 1 2394.5 5.31521
2399.5 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 543.5 4.4149
Subtracted 85 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence 0 6410 6325
21185 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence 1 28492 7307
23818.1 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 0 19621.3 4196.8
41482.5 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 1 33356.5 8126
3 Divided 0.00001 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 0 89 8900000
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 109 10900000
2399.5 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 1 543.5 4.4149
2597.5 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] High confidence 698.5 3.71868
Subtracted 5106.93 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Low confidence 0 7500.75 2393.82
21185 mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 28492 7307
23818.1 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] High confidence 0 19621.3 4196.8
41482.5 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1 33356.5 8126
4 Divided 0.00001 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 0 89 8900000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
2399.5 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 1 543.5 4.4149
2597.5 hbs1-like. [refseq;acc:nm_006620] High confidence 698.5 3.71868
Subtracted 2082 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Low confidence 0 4356 2274
18704 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] High confidence 21730 3026
36474.3 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Low confidence 1 43509.4 7035.1
41482.5 cytohesin 4. [swissprot;acc:q9uia0] High confidence 33356.5 8126
5 Divided 0.00001 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 89 8900000
jumonji protein. [swissprot;acc:q92833] Low confidence 17.5166 1751660
736.5 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 1 2113.5 2.86965
1153.5 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence 339.5 3.39764
Subtracted 485.286 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Low confidence 0 2740.13 2254.84
21773.1 histone h4. [swissprot;acc:p02304] High confidence 24446.3 2673.2
36469.3 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence 1 43503.3 7034
41482.5 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] High confidence 33356.5 8126
6 Divided 0.00001 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 89 8900000
13 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] Low confidence 0.00001 1300000
736.5 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 1 2113.5 2.86965
1153.5 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence 339.5 3.39764
Subtracted 7592.37 similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Low confidence 0 8836.85 1244.48
13174.7 High confidence 15605.1 2430.4
36360.3 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 1 43368.8 7008.5
44490.5 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 36927.5 7563
7 Divided 0.00001 sedlin. [swissprot;acc:o14582] 0 43 4300000
2.31962 tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] Low confidence 0.00001 231962

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/