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 Value Type Rank description red Network Comparison Type green Interaction Map network_comparison Filtered
Results: HTML CSV LaTeX Showing element 1 to 50 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
red
Network Comparison Type
green
network_comparison
Filtered
1 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 4294 Divided 15915 3.70633 0
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 215 Subtracted 322 107 1
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 8906 21883 12977 0
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 10 Divided 24 2.4 1
2 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 4294 Subtracted 15915 11621 0
hbs1-like. [refseq;acc:nm_006620] 215 322 107 1
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] 15 Divided 28 1.86667
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 5865 14977 2.55362 0
3 cab2. [refseq;acc:nm_033419] 21866 Subtracted 10950 10916
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 15 Divided 28 1.86667 1
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 4475.84 11083.9 2.47638 0
rad50-interacting protein 1. [refseq;acc:nm_021930] 337 Subtracted 232 105 1
4 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 15 Divided 28 1.86667
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 8906 21883 2.45711 0
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 11525 Subtracted 21888 10363
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 337 232 105 1
5 cytohesin 4. [swissprot;acc:q9uia0] 15 Divided 28 1.86667
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 11525 Subtracted 21888 10363 0
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 5510.5 Divided 11965.7 2.17144
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 212 Subtracted 309 97 1
6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 15 Divided 28 1.86667
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 5865 Subtracted 14977 9112 0
protein x 0004. [refseq;acc:nm_016301] 212 309 97 1
ubiquitin protein ligase. [refseq;acc:nm_130466] 7523 Divided 15339.2 2.03897 0
7 cab2. [refseq;acc:nm_033419] 21866 10950 1.99689
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 215 322 1.49767 1
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 22286 Subtracted 13216 9070 0
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 288.754 212.554 76.2 1
8 hbs1-like. [refseq;acc:nm_006620] 215 Divided 322 1.49767
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 22286 Subtracted 13216 9070 0
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 288 362 74 1
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 11525 Divided 21888 1.89918 0
9 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 22286 Subtracted 13216 9070
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 288 362 74 1
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 11525 Divided 21888 1.89918 0
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 212 309 1.45755 1
10 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 0
protein x 0004. [refseq;acc:nm_016301] 212 309 1.45755 1
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 20989 Subtracted 12479 8510 0
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] 288 362 74 1
11 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 12170.7 20670.6 8499.9 0
db83 protein. [swissprot;acc:p57088] 288 362 74 1
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 11627 Divided 6248 1.86092 0
rad50-interacting protein 1. [refseq;acc:nm_021930] 337 232 1.45259 1
12 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 9429.18 5208.84 1.81023 0
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 266.856 Subtracted 336.233 69.377 1
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 337 Divided 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] 19403 Subtracted 11267 8136 0
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] 266.856 336.233 69.377 1

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/