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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Gene Rank description Network Comparison Type Value Type Interaction Map Filtered green network_comparison red
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
network_comparison
red
1 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Divided 0 15915 3.70633 4294
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Subtracted 1 322 107 215
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 21883 12977 8906
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Divided 1 24 2.4 10
2 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Subtracted 0 15915 11621 4294
hbs1-like. [refseq;acc:nm_006620] 1 322 107 215
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 1.86667 15
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0 14977 2.55362 5865
3 cab2. [refseq;acc:nm_033419] Subtracted 10950 10916 21866
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Divided 1 28 1.86667 15
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 0 11083.9 2.47638 4475.84
rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted 1 232 105 337
4 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Divided 28 1.86667 15
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 21883 2.45711 8906
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Subtracted 21888 10363 11525
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 232 105 337
5 cytohesin 4. [swissprot;acc:q9uia0] Divided 28 1.86667 15
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Subtracted 0 21888 10363 11525
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Divided 11965.7 2.17144 5510.5
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Subtracted 1 309 97 212
6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Divided 28 1.86667 15
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted 0 14977 9112 5865
protein x 0004. [refseq;acc:nm_016301] 1 309 97 212
ubiquitin protein ligase. [refseq;acc:nm_130466] Divided 0 15339.2 2.03897 7523
7 cab2. [refseq;acc:nm_033419] 10950 1.99689 21866
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 322 1.49767 215
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 0 13216 9070 22286
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 212.554 76.2 288.754
8 hbs1-like. [refseq;acc:nm_006620] Divided 322 1.49767 215
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 0 13216 9070 22286
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 362 74 288
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 0 21888 1.89918 11525
9 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 13216 9070 22286
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 362 74 288
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided 0 21888 1.89918 11525
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 309 1.45755 212
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 1.88805 7509.39
protein x 0004. [refseq;acc:nm_016301] 1 309 1.45755 212
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Subtracted 0 12479 8510 20989
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 74 288
11 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 0 20670.6 8499.9 12170.7
db83 protein. [swissprot;acc:p57088] 1 362 74 288
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 0 6248 1.86092 11627
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 232 1.45259 337
12 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 0 5208.84 1.81023 9429.18
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Subtracted 1 336.233 69.377 266.856
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided 232 1.45259 337
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 8136 19403
13 dystrophin. [swissprot;acc:p11532] 18054.8 7822.3 10232.5
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 1 336.233 69.377 266.856

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/