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 Value Type Rank Network Comparison Type green red Filtered description Interaction Map network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 77072 in total
Value Type  : Measured
Rank
Network Comparison Type
green
red
Filtered
description
Interaction Map
network_comparison
1 Divided 0.00001 364 0 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 36400000
Low confidence
543.5 2399.5 1 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 4.4149
2394.5 450.5 rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 5.31521
Subtracted 6410 85 0 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 6325
Low confidence
32028.5 40899 1 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 8870.5
33356.5 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 8126
2 Divided 89 0.00001 0 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 8900000
174 cab2. [refseq;acc:nm_033419] High confidence 17400000
543.5 2399.5 1 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 4.4149
2394.5 450.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 5.31521
Subtracted 6410 85 0 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 6325
19621.3 23818.1 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 4196.8
28492 21185 1 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 7307
33356.5 41482.5 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 8126
3 Divided 89 0.00001 0 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 8900000
109 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 10900000
543.5 2399.5 1 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 4.4149
698.5 2597.5 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] High confidence 3.71868
Subtracted 7500.75 5106.93 0 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Low confidence 2393.82
19621.3 23818.1 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] High confidence 4196.8
28492 21185 1 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence 7307
33356.5 41482.5 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 8126
4 Divided 89 0.00001 0 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 8900000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
543.5 2399.5 1 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 4.4149
698.5 2597.5 hbs1-like. [refseq;acc:nm_006620] High confidence 3.71868
Subtracted 4356 2082 0 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Low confidence 2274
21730 18704 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] High confidence 3026
33356.5 41482.5 1 cytohesin 4. [swissprot;acc:q9uia0] 8126
43509.4 36474.3 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Low confidence 7035.1
5 Divided 17.5166 0.00001 0 jumonji protein. [swissprot;acc:q92833] 1751660
89 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 8900000
339.5 1153.5 1 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 3.39764
2113.5 736.5 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 2.86965
Subtracted 2740.13 485.286 0 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 2254.84
24446.3 21773.1 histone h4. [swissprot;acc:p02304] High confidence 2673.2
33356.5 41482.5 1 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 8126
43503.3 36469.3 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence 7034
6 Divided 0.00001 13 0 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 1300000
89 0.00001 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 8900000
339.5 1153.5 1 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 3.39764
2113.5 736.5 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 2.86965
Subtracted 8836.85 7592.37 0 similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 1244.48
15605.1 13174.7 High confidence 2430.4
36927.5 44490.5 1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 7563
43368.8 36360.3 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 7008.5
7 Divided 0.00001 2.31962 0 tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] 231962
43 0.00001 sedlin. [swissprot;acc:o14582] High confidence 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/