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 Rank Value Type Network Comparison Type Interaction Map description Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
Network Comparison Type
description
Filtered
red
green
network_comparison
13 Subtracted dystrophin. [swissprot;acc:p11532] 0 10232.5 18054.8 7822.3
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 1 266.856 336.233 69.377
14 Divided cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 56.6768 75.3531 1.32952
dystrophin. [swissprot;acc:p11532] 0 10232.5 18054.8 1.76446
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 1 266.863 336.191 69.328
ubiquitin protein ligase. [refseq;acc:nm_130466] 0 7523 15339.2 7816.2
15 Divided microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 1 56.7244 75.3948 1.32914
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] 0 19403 11267 1.72211
Subtracted 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] 22422 14964 7458
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 1 266.863 336.19 69.327
16 Divided cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 0 12170.7 20670.6 1.69839
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 1 56.7252 75.3954 1.32913
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 266.864 336.184 69.32
ptd016 protein. [refseq;acc:nm_016125] 0 18050 11234 6816
17 Divided cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 1 56.7841 75.447 1.32866
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 0 11543 6812 1.69451
Subtracted ero1-like. [refseq;acc:nm_014584] 13853 20536 6683
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 1 266.864 336.182 69.318
18 Divided 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 185.678 245.247 1.32082
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 22286 13216 1.68629
Subtracted fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 7509.39 14178.1 6668.71
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1 266.865 336.181 69.316
19 Divided glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 185.678 245.247 1.32082
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 22286 13216 1.68629
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 1 266.865 336.178 69.313
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 0 4475.84 11083.9 6608.06
20 Divided glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1 185.678 245.247 1.32082
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 22286 13216 1.68629
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 1 266.868 336.159 69.291
serpin b12. [swissprot;acc:q96p63] 0 14604.2 21138.6 6534.4
21 Divided acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 6313.38 10621.4 1.68236
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 1 185.678 245.247 1.32082
Subtracted gbp protein isoform a. [refseq;acc:nm_017870] 325.586 256.492 69.094
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 0 14592 21113.7 6521.7
22 Divided glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1 185.678 245.247 1.32082
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 20989 12479 1.68195
Subtracted protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 1 322 253 69
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 0 5510.5 11965.7 6455.2
23 Divided 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1 58 44 1.31818
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 0 15520.4 9285.44 1.67148
Subtracted 6234.96
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 1 322 253 69
24 Divided ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 13730.5 8257 1.66289
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 1 58 44 1.31818
Subtracted protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 322 253 69
sedlin. [swissprot;acc:o14582] 0 22440 16388 6052
25 Divided lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 13730.5 8257 1.66289
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 1 58 44 1.31818
Subtracted ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 322 253 69
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 0 22440 16388 6052

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/