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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Gene Value Type Network Comparison Type Filtered Rank description Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 77072 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 0
Rank
description
Interaction Map
red
green
network_comparison
1 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 364 0.00001 36400000
Low confidence
2 cab2. [refseq;acc:nm_033419] High confidence 0.00001 174 17400000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 89 8900000
3 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 109 10900000
4 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 89 8900000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
5 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
jumonji protein. [swissprot;acc:q92833] Low confidence 17.5166 1751660
6 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 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
7 sedlin. [swissprot;acc:o14582] High confidence 0.00001 43 4300000
tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] Low confidence 2.31962 0.00001 231962
8 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 85 6410 75.4118
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] High confidence 0.00001 43 4300000
9 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 85 6410 75.4118
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 383.762 10.6048 36.1876
10 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence 85 6410 75.4118
serpin b12. [swissprot;acc:q96p63] Low confidence 199.549 5.56738 35.8425
11 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 199.249 5.71669 34.8539
serpin b12. [swissprot;acc:q96p63] High confidence 199.549 5.56738 35.8425
12 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 199.249 5.71669 34.8539
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Low confidence 859 58 14.8103
13 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] High confidence 1363 47 29
fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] Low confidence 8.11997 115.385 14.21
14 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] High confidence 130.512 6.50325 20.0687
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] Low confidence 0.00001 59 5900000
15 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 485.286 2740.13 5.64642
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] High confidence 10 156 15.6
16 protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Low confidence 125 704.5 5.636
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] High confidence 1 15 15
17 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 859 58 14.8103
ptd016 protein. [refseq;acc:nm_016125] Low confidence 30 158 5.26667
18 60s ribosomal protein l37a. [swissprot;acc:p12751] High confidence 305.45 26.1599 11.6763
camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Low confidence 99 19 5.21053
19 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] High confidence 305.45 26.1599 11.6763
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Low confidence 153 662 4.3268
20 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 570 139 4.10072
ero1-like. [refseq;acc:nm_014584] High confidence 82 0.00001 8200000
21 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Low confidence 111.278 434.911 3.90833
syntaxin 10 (syn10). [swissprot;acc:o60499] High confidence 118.878 17.6611 6.73106
22 carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615] Low confidence 37 0.00001 3700000
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] High confidence 60 6000000
23 carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] Low confidence 37 3700000
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] High confidence 0.00001 59 5900000
24 cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Low confidence 154 493 3.2013
ptd016 protein. [refseq;acc:nm_016125] High confidence 30 158 5.26667
25 lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Low confidence 12.6208 39.8063 3.15402
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] High confidence 148 773 5.22297

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/