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 Network Comparison Type Rank description green Interaction Map network_comparison Filtered red
Results: HTML CSV LaTeX Showing element 1 to 50 of 7460 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
green
network_comparison
Filtered
red
1 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 15915 3.70633 0 4294
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 24 2.4 1 10
2 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] 28 1.86667 15
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14977 2.55362 0 5865
3 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 28 1.86667 1 15
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 11083.9 2.47638 0 4475.84
4 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 28 1.86667 1 15
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 21883 2.45711 0 8906
5 cytohesin 4. [swissprot;acc:q9uia0] 28 1.86667 1 15
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 11965.7 2.17144 0 5510.5
6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 28 1.86667 1 15
ubiquitin protein ligase. [refseq;acc:nm_130466] 15339.2 2.03897 0 7523
7 cab2. [refseq;acc:nm_033419] 10950 1.99689 21866
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 322 1.49767 1 215
8 hbs1-like. [refseq;acc:nm_006620]
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 21888 1.89918 0 11525
9 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 309 1.45755 1 212
10 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 0 7509.39
protein x 0004. [refseq;acc:nm_016301] 309 1.45755 1 212
11 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 6248 1.86092 0 11627
rad50-interacting protein 1. [refseq;acc:nm_021930] 232 1.45259 1 337
12 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 5208.84 1.81023 0 9429.18
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 232 1.45259 1 337
13 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 9264.5 1.77804 0 5210.5
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 212.554 1.3585 1 288.754
14 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 75.3531 1.32952 56.6768
dystrophin. [swissprot;acc:p11532] 18054.8 1.76446 0 10232.5
15 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 75.3948 1.32914 1 56.7244
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] 11267 1.72211 0 19403
16 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 20670.6 1.69839 12170.7
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 75.3954 1.32913 1 56.7252
17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 75.447 1.32866 56.7841
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 6812 1.69451 0 11543
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 245.247 1.32082 1 185.678
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 13216 1.68629 0 22286
19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 245.247 1.32082 1 185.678
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 13216 1.68629 0 22286
20 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 245.247 1.32082 1 185.678
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 13216 1.68629 0 22286
21 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 10621.4 1.68236 6313.38
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 245.247 1.32082 1 185.678
22 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 12479 1.68195 0 20989
23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 44 1.31818 1 58
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 9285.44 1.67148 0 15520.4
24 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 8257 1.66289 13730.5
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 44 1.31818 1 58
25 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 8257 1.66289 0 13730.5
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 44 1.31818 1 58

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/