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 green red network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
green
red
network_comparison
1 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Divided 0 15915 4294 3.70633
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Subtracted 1 322 215 107
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 21883 8906 12977
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Divided 1 24 10 2.4
2 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Subtracted 0 15915 4294 11621
hbs1-like. [refseq;acc:nm_006620] 1 322 215 107
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 28 15 1.86667
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0 14977 5865 2.55362
3 cab2. [refseq;acc:nm_033419] Subtracted 10950 21866 10916
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Divided 1 28 15 1.86667
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 0 11083.9 4475.84 2.47638
rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted 1 232 337 105
4 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Divided 28 15 1.86667
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 21883 8906 2.45711
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Subtracted 21888 11525 10363
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 232 337 105
5 cytohesin 4. [swissprot;acc:q9uia0] Divided 28 15 1.86667
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Subtracted 0 21888 11525 10363
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Divided 11965.7 5510.5 2.17144
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Subtracted 1 309 212 97
6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Divided 28 15 1.86667
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted 0 14977 5865 9112
protein x 0004. [refseq;acc:nm_016301] 1 309 212 97
ubiquitin protein ligase. [refseq;acc:nm_130466] Divided 0 15339.2 7523 2.03897
7 cab2. [refseq;acc:nm_033419] 10950 21866 1.99689
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 322 215 1.49767
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 0 13216 22286 9070
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 212.554 288.754 76.2
8 hbs1-like. [refseq;acc:nm_006620] Divided 322 215 1.49767
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 0 13216 22286 9070
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 362 288 74
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 0 21888 11525 1.89918
9 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 13216 22286 9070
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 362 288 74
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided 0 21888 11525 1.89918
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 309 212 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 14178.1 7509.39 1.88805
protein x 0004. [refseq;acc:nm_016301] 1 309 212 1.45755
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Subtracted 0 12479 20989 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] 1 362 288 74
11 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 0 20670.6 12170.7 8499.9
db83 protein. [swissprot;acc:p57088] 1 362 288 74
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 0 6248 11627 1.86092
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 232 337 1.45259
12 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 0 5208.84 9429.18 1.81023
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Subtracted 1 336.233 266.856 69.377
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided 232 337 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 11267 19403 8136
13 dystrophin. [swissprot;acc:p11532] 18054.8 10232.5 7822.3
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 1 336.233 266.856 69.377

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/