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