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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Filtered Rank description Gene green Network Comparison Type Value Type red Interaction Map network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 14920 in total
Filtered  : 0
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
green
Value Type
red
network_comparison
13 dok-like protein. [refseq;acc:nm_024872] 0.00001 Rooted 5.91608 591608
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 9264.5 Ranked 5210.5 1.77804
14 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 19295.9 Squared 1.73869 11098
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 6.50325 Measured 130.512 20.0687
dystrophin. [swissprot;acc:p11532] 18054.8 Ranked 10232.5 1.76446
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 4.24264 Rooted 0.00001 424264
15 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 19295.9 Squared 1.73869 11098
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0.00001 Rooted 4.24264 424264
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] 156 Measured 10 15.6
11267 Ranked 19403 1.72211
16 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 20670.6 12170.7 1.69839
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 0.0766864 Squared 0.00001 7668.64
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 15 Measured 1 15
serpin b12. [swissprot;acc:q96p63] 1.18697 Rooted 10.2928 8.67149
17 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 6812 Ranked 11543 1.69451
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 1.2188 Rooted 10.3085 8.45791
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 58 Measured 859 14.8103
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0.00001 Squared 0.0766864 7668.64
18 60s ribosomal protein l37a. [swissprot;acc:p12751] 26.1599 Measured 305.45 11.6763
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 0.52284 Squared 439.709 841.001
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 60.0707 Rooted 9.20014 6.52932
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 13216 Ranked 22286 1.68629
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] 26.1599 Measured 305.45 11.6763
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 13216 Ranked 22286 1.68629
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 60.0707 Rooted 9.20014 6.52932
serpin b12. [swissprot;acc:q96p63] 0.0289898 Squared 23.5744 813.196
20 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 1.80368 Rooted 11.3774 6.30788
ero1-like. [refseq;acc:nm_014584] 0.00001 Measured 82 8200000
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 13216 Ranked 22286 1.68629
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 0.0297673 Squared 23.4957 789.312
21 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 10621.4 Ranked 6313.38 1.68236
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 6.85565 Rooted 36.9188 5.38516
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] 5.76 Squared 0.0236686 243.36
syntaxin 10 (syn10). [swissprot;acc:o60499] 17.6611 Measured 118.878 6.73106
22 protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 0.0532544 Squared 0.000236686 225
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 12479 Ranked 20989 1.68195
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 0.00001 Measured 60 6000000
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] 12.49 Rooted 3.16228 3.94968
23 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] 59 Measured 0.00001 5900000
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 9285.44 Ranked 15520.4 1.67148
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0.796213 Squared 174.646 219.346
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 3.87298 Rooted 1 3.87298
24 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 8257 Ranked 13730.5 1.66289
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 0.02001 Squared 4.16226 208.009
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 7.61577 Rooted 29.3087 3.84842
ptd016 protein. [refseq;acc:nm_016125] 158 Measured 30 5.26667
25 60s ribosomal protein l37a. [swissprot;acc:p12751] 0.344399 Squared 44.3683 128.828
3.80565 Rooted 13.7805 3.62106
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 8257 Ranked 13730.5 1.66289
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 773 Measured 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/