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 Interaction Map Filtered description Value Type Network Comparison Type red green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 7460 in total
Interaction Map  : High confidence
Value Type  : Ranked
Rank
Filtered
description
Network Comparison Type
red
green
network_comparison
1 0 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Divided 4294 15915 3.70633
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Subtracted 8906 21883 12977
1 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 215 322 107
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Divided 10 24 2.4
2 0 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Subtracted 4294 15915 11621
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Divided 5865 14977 2.55362
1 hbs1-like. [refseq;acc:nm_006620] Subtracted 215 322 107
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 15 28 1.86667
3 0 cab2. [refseq;acc:nm_033419] Subtracted 21866 10950 10916
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Divided 4475.84 11083.9 2.47638
1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 15 28 1.86667
rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted 337 232 105
4 0 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 8906 21883 2.45711
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Subtracted 11525 21888 10363
1 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Divided 15 28 1.86667
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Subtracted 337 232 105
5 0 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 11525 21888 10363
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Divided 5510.5 11965.7 2.17144
1 cytohesin 4. [swissprot;acc:q9uia0] 15 28 1.86667
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Subtracted 212 309 97
6 0 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 5865 14977 9112
ubiquitin protein ligase. [refseq;acc:nm_130466] Divided 7523 15339.2 2.03897
1 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 15 28 1.86667
protein x 0004. [refseq;acc:nm_016301] Subtracted 212 309 97
7 0 cab2. [refseq;acc:nm_033419] Divided 21866 10950 1.99689
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 22286 13216 9070
1 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Divided 215 322 1.49767
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Subtracted 288.754 212.554 76.2
8 0 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 22286 13216 9070
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 11525 21888 1.89918
1 hbs1-like. [refseq;acc:nm_006620] 215 322 1.49767
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Subtracted 288 362 74
9 0 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 22286 13216 9070
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided 11525 21888 1.89918
1 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Subtracted 288 362 74
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Divided 212 309 1.45755
10 0 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 1.88805
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Subtracted 20989 12479 8510
1 protein x 0004. [refseq;acc:nm_016301] Divided 212 309 1.45755
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] Subtracted 288 362 74
11 0 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 12170.7 20670.6 8499.9
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 11627 6248 1.86092
1 db83 protein. [swissprot;acc:p57088] Subtracted 288 362 74
rad50-interacting protein 1. [refseq;acc:nm_021930] Divided 337 232 1.45259
12 0 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 9429.18 5208.84 1.81023
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 19403 11267 8136
1 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 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
13 0 dystrophin. [swissprot;acc:p11532] Subtracted 10232.5 18054.8 7822.3
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Divided 5210.5 9264.5 1.77804

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/