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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 red Network Comparison Type description Interaction Map Filtered green Value Type network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
Value Type  : Measured
Rank
red
Network Comparison Type
description
Interaction Map
Filtered
green
network_comparison
1 85 Subtracted ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] High confidence 0 6410 6325
Low confidence
364 Divided mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 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
40899 Subtracted carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 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 0.00001 Divided cab2. [refseq;acc:nm_033419] 0 174 17400000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 89 8900000
85 Subtracted lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence 6410 6325
450.5 Divided rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 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
21185 Subtracted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 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 0.00001 Divided 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
5106.93 Subtracted 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 0.00001 Divided 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
2082 Subtracted anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Low confidence 4356 2274
2399.5 Divided lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 1 543.5 4.4149
2597.5 hbs1-like. [refseq;acc:nm_006620] High confidence 698.5 3.71868
18704 Subtracted small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 0 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 0.00001 Divided 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
485.286 Subtracted lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 2740.13 2254.84
736.5 Divided 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
21773.1 Subtracted histone h4. [swissprot;acc:p02304] 0 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 0.00001 Divided 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
7592.37 Subtracted 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 0.00001 Divided 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/