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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 151 to 200 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
38 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Ranked 322 253 1.27273
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Squared 106226 192141 1.80879
39 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Measured 1836.8 907.903 2.02312
Rooted 40.28 24.37 1.65285
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Squared 106226 192141 1.80879
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Ranked 322 253 1.27273
40 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Squared 144940 81169.7 1.78564
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Ranked 322 253 1.27273
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Measured 1836.81 907.978 2.02297
Rooted 40.2797 24.3705 1.65281
41 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Measured 1836.81 907.978 2.02297
Rooted 40.2797 24.3705 1.65281
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Squared 144912 81155 1.78562
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Ranked 322 253 1.27273
42 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Measured 1857.32 958.237 1.93827
Rooted 40.225 24.7051 1.62821
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Squared 144911 81154.7 1.78561
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked 204.641 160.957 1.2714
43 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared 144876 81136.5 1.78558
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Rooted 40.6302 25.4452 1.59677
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Measured 1881.02 1027.36 1.83093
jun dimerization protein. [refseq;acc:nm_130469] Ranked 204.641 160.957 1.2714
44 fos-related antigen 2. [swissprot;acc:p15408] 161.046 1.2707
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared 139741 78454.6 1.78117
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Rooted 40.5691 25.4263 1.59556
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Measured 1931.34 1057.39 1.82652
45 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Squared 129597 73157.5 1.77148
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Measured 1926.69 1056.02 1.82448
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Rooted 40.081 25.1546 1.59339
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked 204.641 161.051 1.27066
46 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared 129597 73157.5 1.77148
deltex 2. [refseq;acc:nm_020892] Rooted 27.634 43.9629 1.5909
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 204.642 161.068 1.27053
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Measured 779.167 1390.33 1.78438
47 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted 27.7078 44.017 1.58861
gbp protein isoform a. [refseq;acc:nm_017870] Ranked 325.586 256.492 1.26938
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Squared 98517.9 56927.2 1.73059
48 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Measured 779.167 1390.33 1.78438
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Ranked 65.4586 83.0461 1.26868
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Squared 6300.2 10703.5 1.69891
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Rooted 27.7254 44.0299 1.58807
49 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared 28994.2 17134.8 1.69212
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Ranked 133 105 1.26667
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Rooted 27.7254 44.0299 1.58807
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Measured 779.167 1390.33 1.78438
50 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Ranked 133 105 1.26667
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Rooted 27.7254 44.0299 1.58807
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured 779.167 1390.33 1.78438
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Squared 28994.2 17134.8 1.69212

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/