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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Value Type Rank Filtered description Gene Network Comparison Type green Interaction Map network_comparison red
Results: HTML CSV LaTeX Showing element 1 to 50 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
Filtered
description
Network Comparison Type
green
network_comparison
red
1 0 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Divided 15915 3.70633 4294
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Subtracted 21883 12977 8906
1 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 322 107 215
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Divided 24 2.4 10
2 0 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Subtracted 15915 11621 4294
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Divided 14977 2.55362 5865
1 hbs1-like. [refseq;acc:nm_006620] Subtracted 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
3 0 cab2. [refseq;acc:nm_033419] Subtracted 10950 10916 21866
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Divided 11083.9 2.47638 4475.84
1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 28 1.86667 15
rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted 232 105 337
4 0 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 21883 2.45711 8906
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Subtracted 21888 10363 11525
1 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Divided 28 1.86667 15
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Subtracted 232 105 337
5 0 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 21888 10363 11525
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Divided 11965.7 2.17144 5510.5
1 cytohesin 4. [swissprot;acc:q9uia0] 28 1.86667 15
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Subtracted 309 97 212
6 0 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14977 9112 5865
ubiquitin protein ligase. [refseq;acc:nm_130466] Divided 15339.2 2.03897 7523
1 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 28 1.86667 15
protein x 0004. [refseq;acc:nm_016301] Subtracted 309 97 212
7 0 cab2. [refseq;acc:nm_033419] Divided 10950 1.99689 21866
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 13216 9070 22286
1 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Divided 322 1.49767 215
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Subtracted 212.554 76.2 288.754
8 0 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 13216 9070 22286
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 21888 1.89918 11525
1 hbs1-like. [refseq;acc:nm_006620] 322 1.49767 215
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Subtracted 362 74 288
9 0 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 13216 9070 22286
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided 21888 1.89918 11525
1 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Subtracted 362 74 288
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Divided 309 1.45755 212
10 0 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 14178.1 1.88805 7509.39
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Subtracted 12479 8510 20989
1 protein x 0004. [refseq;acc:nm_016301] Divided 309 1.45755 212
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 362 74 288
11 0 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 20670.6 8499.9 12170.7
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 6248 1.86092 11627
1 db83 protein. [swissprot;acc:p57088] Subtracted 362 74 288
rad50-interacting protein 1. [refseq;acc:nm_021930] Divided 232 1.45259 337
12 0 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 5208.84 1.81023 9429.18
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 11267 8136 19403
1 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 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
13 0 dystrophin. [swissprot;acc:p11532] Subtracted 18054.8 7822.3 10232.5
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Divided 9264.5 1.77804 5210.5

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/