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 Value Type Rank description red green Network Comparison Type Interaction Map network_comparison Filtered
Results: HTML CSV LaTeX Showing element 51 to 100 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
red
green
Network Comparison Type
network_comparison
Filtered
13 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 5210.5 9264.5 Divided 1.77804 0
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 288.754 212.554 1.3585 1
14 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 56.6768 75.3531 1.32952
dystrophin. [swissprot;acc:p11532] 10232.5 18054.8 1.76446 0
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 266.863 336.191 Subtracted 69.328 1
ubiquitin protein ligase. [refseq;acc:nm_130466] 7523 15339.2 7816.2 0
15 guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 22422 14964 7458
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 266.863 336.19 69.327 1
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 56.7244 75.3948 Divided 1.32914
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 11267 1.72211 0
16 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 12170.7 20670.6 1.69839
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 266.864 336.184 Subtracted 69.32 1
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 56.7252 75.3954 Divided 1.32913
ptd016 protein. [refseq;acc:nm_016125] 18050 11234 Subtracted 6816 0
17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 56.7841 75.447 Divided 1.32866 1
ero1-like. [refseq;acc:nm_014584] 13853 20536 Subtracted 6683 0
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 11543 6812 Divided 1.69451
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 266.864 336.182 Subtracted 69.318 1
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 185.678 245.247 Divided 1.32082
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 Subtracted 6668.71 0
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 266.865 336.181 69.316 1
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 22286 13216 Divided 1.68629 0
19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 185.678 245.247 1.32082 1
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 266.865 336.178 Subtracted 69.313
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 22286 13216 Divided 1.68629 0
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 4475.84 11083.9 Subtracted 6608.06
20 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 185.678 245.247 Divided 1.32082 1
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 266.868 336.159 Subtracted 69.291
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 22286 13216 Divided 1.68629 0
serpin b12. [swissprot;acc:q96p63] 14604.2 21138.6 Subtracted 6534.4
21 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 6313.38 10621.4 Divided 1.68236
gbp protein isoform a. [refseq;acc:nm_017870] 325.586 256.492 Subtracted 69.094 1
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 14592 21113.7 6521.7 0
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 185.678 245.247 Divided 1.32082 1
22 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 322 253 Subtracted 69
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 20989 12479 Divided 1.68195 0
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 5510.5 11965.7 Subtracted 6455.2
23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 58 44 Divided 1.31818 1
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 15520.4 9285.44 1.67148 0
Subtracted 6234.96
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 322 253 69 1
24 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 13730.5 8257 Divided 1.66289 0
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 58 44 1.31818 1
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 322 253 Subtracted 69
sedlin. [swissprot;acc:o14582] 22440 16388 6052 0
25 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 322 253 69 1
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 13730.5 8257 Divided 1.66289 0
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 58 44 1.31818 1
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 22440 16388 Subtracted 6052 0

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/