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 Interaction Map Value Type Network Comparison Type Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1 to 50 of 7460 in total
Interaction Map  : High confidence
Value Type  : Ranked
Rank
description
Network Comparison Type
Filtered
red
network_comparison
green
1 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Divided 0 4294 3.70633 15915
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Subtracted 1 215 107 322
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 8906 12977 21883
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Divided 1 10 2.4 24
2 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Subtracted 0 4294 11621 15915
hbs1-like. [refseq;acc:nm_006620] 1 215 107 322
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Divided 15 1.86667 28
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0 5865 2.55362 14977
3 cab2. [refseq;acc:nm_033419] Subtracted 21866 10916 10950
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Divided 1 15 1.86667 28
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 0 4475.84 2.47638 11083.9
rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted 1 337 105 232
4 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Divided 15 1.86667 28
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 8906 2.45711 21883
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Subtracted 11525 10363 21888
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 337 105 232
5 cytohesin 4. [swissprot;acc:q9uia0] Divided 15 1.86667 28
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Subtracted 0 11525 10363 21888
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Divided 5510.5 2.17144 11965.7
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Subtracted 1 212 97 309
6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Divided 15 1.86667 28
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted 0 5865 9112 14977
protein x 0004. [refseq;acc:nm_016301] 1 212 97 309
ubiquitin protein ligase. [refseq;acc:nm_130466] Divided 0 7523 2.03897 15339.2
7 cab2. [refseq;acc:nm_033419] 21866 1.99689 10950
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 215 1.49767 322
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 0 22286 9070 13216
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 288.754 76.2 212.554
8 hbs1-like. [refseq;acc:nm_006620] Divided 215 1.49767 322
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 0 22286 9070 13216
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 288 74 362
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 0 11525 1.89918 21888
9 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 22286 9070 13216
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 288 74 362
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided 0 11525 1.89918 21888
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 212 1.45755 309
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 1.88805 14178.1
protein x 0004. [refseq;acc:nm_016301] 1 212 1.45755 309
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Subtracted 0 20989 8510 12479
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 74 362
11 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 0 12170.7 8499.9 20670.6
db83 protein. [swissprot;acc:p57088] 1 288 74 362
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 0 11627 1.86092 6248
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 337 1.45259 232
12 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 0 9429.18 1.81023 5208.84
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Subtracted 1 266.856 69.377 336.233
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided 337 1.45259 232
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 8136 11267
13 dystrophin. [swissprot;acc:p11532] 10232.5 7822.3 18054.8
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 1 266.856 69.377 336.233

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/