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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 130 to 179 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
17 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Measured 1 460 1365 2.96739
Squared 50.0828 441 8.80542
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Ranked 0 11543 6812 1.69451
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Rooted 10.3085 1.2188 8.45791
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Measured 859 58 14.8103
protein x 0004. [refseq;acc:nm_016301] Rooted 1 51.6817 29.5127 1.75117
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Squared 0 0.0766864 0.00001 7668.64
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Ranked 1 185.678 245.247 1.32082
60s ribosomal protein l37a. [swissprot;acc:p12751] Measured 0 305.45 26.1599 11.6763
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Squared 439.709 0.52284 841.001
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Rooted 9.20014 60.0707 6.52932
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 1 21.4476 36.9459 1.72261
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Ranked 0 22286 13216 1.68629
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Measured 1 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
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] Measured 0 305.45 26.1599 11.6763
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked 1 185.678 245.247 1.32082
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 22286 13216 1.68629
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Rooted 9.20014 60.0707 6.52932
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Measured 1 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Rooted 25.6987 43.561 1.69507
serpin b12. [swissprot;acc:q96p63] Squared 0 23.5744 0.0289898 813.196
20 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Rooted 11.3774 1.80368 6.30788
ero1-like. [refseq;acc:nm_014584] Measured 82 0.00001 8200000
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Ranked 1 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Rooted 40.3337 24.2744 1.66157
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Ranked 0 22286 13216 1.68629
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Squared 23.4957 0.0297673 789.312
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Measured 1 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
21 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Ranked 0 6313.38 10621.4 1.68236
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Rooted 36.9188 6.85565 5.38516
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Measured 1 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Rooted 40.3337 24.2744 1.66157
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Ranked 185.678 245.247 1.32082
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] Squared 0 0.0236686 5.76 243.36
syntaxin 10 (syn10). [swissprot;acc:o60499] Measured 118.878 17.6611 6.73106
22 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Ranked 1 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Rooted 40.3357 24.2915 1.66049
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Measured 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 0 0.000236686 0.0532544 225
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Ranked 20989 12479 1.68195
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] Measured 60 0.00001 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] Rooted 3.16228 12.49 3.94968
23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Ranked 1 58 44 1.31818
gbp protein isoform a. [refseq;acc:nm_017870] Measured 699.76 1894.39 2.7072
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] 0 0.00001 59 5900000

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/