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 Filtered Rank description Network Comparison Type Value Type Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 9634 in total
Filtered  : 0
Network Comparison Type  : Divided
Value Type  : Measured
Rank
description
Interaction Map
green
red
network_comparison
1 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 0.00001 364 36400000
Low confidence
2 cab2. [refseq;acc:nm_033419] High confidence 174 0.00001 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 0.00001 13 1300000
7 sedlin. [swissprot;acc:o14582] High confidence 43 0.00001 4300000
tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] Low confidence 0.00001 2.31962 231962
8 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 6410 85 75.4118
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] High confidence 43 0.00001 4300000
9 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 6410 85 75.4118
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 10.6048 383.762 36.1876
10 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence 6410 85 75.4118
serpin b12. [swissprot;acc:q96p63] Low confidence 5.56738 199.549 35.8425
11 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 5.71669 199.249 34.8539
serpin b12. [swissprot;acc:q96p63] High confidence 5.56738 199.549 35.8425
12 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 5.71669 199.249 34.8539
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Low confidence 58 859 14.8103
13 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] High confidence 47 1363 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 115.385 8.11997 14.21
14 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] High confidence 6.50325 130.512 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 59 0.00001 5900000
15 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 2740.13 485.286 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 156 10 15.6
16 protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Low confidence 704.5 125 5.636
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] High confidence 15 1 15
17 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 58 859 14.8103
ptd016 protein. [refseq;acc:nm_016125] Low confidence 158 30 5.26667
18 60s ribosomal protein l37a. [swissprot;acc:p12751] High confidence 26.1599 305.45 11.6763
camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Low confidence 19 99 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 26.1599 305.45 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 662 153 4.3268
20 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 139 570 4.10072
ero1-like. [refseq;acc:nm_014584] High confidence 0.00001 82 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 434.911 111.278 3.90833
syntaxin 10 (syn10). [swissprot;acc:o60499] High confidence 17.6611 118.878 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 0.00001 37 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 59 0.00001 5900000
24 cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Low confidence 493 154 3.2013
ptd016 protein. [refseq;acc:nm_016125] High confidence 158 30 5.26667
25 lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Low confidence 39.8063 12.6208 3.15402
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] High confidence 773 148 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/