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 30 to 79 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
8 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 0 22286 13216 9070
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 288 362 74
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 0 11525 21888 1.89918
9 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 22286 13216 9070
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 288 362 74
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided 0 11525 21888 1.89918
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 212 309 1.45755
10 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 0 7509.39 14178.1 1.88805
protein x 0004. [refseq;acc:nm_016301] 1 212 309 1.45755
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Subtracted 0 20989 12479 8510
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 1 288 362 74
11 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 0 12170.7 20670.6 8499.9
db83 protein. [swissprot;acc:p57088] 1 288 362 74
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 0 11627 6248 1.86092
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 337 232 1.45259
12 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 0 9429.18 5208.84 1.81023
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Subtracted 1 266.856 336.233 69.377
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided 337 232 1.45259
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] Subtracted 0 19403 11267 8136
13 dystrophin. [swissprot;acc:p11532] 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
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Divided 0 5210.5 9264.5 1.77804
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 288.754 212.554 1.3585
14 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
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Subtracted 1 266.863 336.191 69.328
ubiquitin protein ligase. [refseq;acc:nm_130466] 0 7523 15339.2 7816.2
15 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
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Divided 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
16 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 12170.7 20670.6 1.69839
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Subtracted 1 266.864 336.184 69.32
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Divided 56.7252 75.3954 1.32913
ptd016 protein. [refseq;acc:nm_016125] Subtracted 0 18050 11234 6816
17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Divided 1 56.7841 75.447 1.32866
ero1-like. [refseq;acc:nm_014584] Subtracted 0 13853 20536 6683
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Divided 11543 6812 1.69451
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Subtracted 1 266.864 336.182 69.318
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Divided 185.678 245.247 1.32082
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Subtracted 0 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
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 0 22286 13216 1.68629
19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 266.865 336.178 69.313
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 0 22286 13216 1.68629
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Subtracted 4475.84 11083.9 6608.06
20 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Divided 1 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Subtracted 266.868 336.159 69.291
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Divided 0 22286 13216 1.68629

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/