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 173 to 222 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
44 fos-related antigen 2. [swissprot;acc:p15408] Ranked 204.641 161.046 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
51 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Rooted 27.7254 44.0299 1.58807
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 1390.33 1.78438
spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 133 105 1.26667
52 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Measured 779.167 1390.33 1.78438
neuralized-like. [refseq;acc:nm_004210] Rooted 27.9107 44.1656 1.58239
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared 28994.2 17134.8 1.69212
53 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Measured 779.167 1390.33 1.78438
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Rooted 30.8986 46.4619 1.50369
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 28994.2 17134.8 1.69212
transcription factor jun-b. [swissprot;acc:p17275] Ranked 201.144 158.868 1.26611
54 deltex 2. [refseq;acc:nm_020892] Measured 1618.84 2651.88 1.63814
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Squared 219048 129762 1.68808
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Rooted 40.0958 58.7986 1.46645
transcription factor jun-d. [swissprot;acc:p17535] Ranked 200.941 158.941 1.26425
55 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured 1629.21 2662.12 1.63399
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Squared 219048 129762 1.68808
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Rooted 41.6734 28.9323 1.44038
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Ranked 320.927 254.434 1.26134
56 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 41.6851 28.9509 1.43986
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Ranked 266.856 336.233 1.25998

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/