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 Interaction Map Value Type Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 401 to 450 of 7460 in total
Interaction Map  : High confidence
Value Type  : Ranked
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
101 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Subtracted 0 12577.8 14662.1 2084.3
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Divided 14548.5 11915.2 1.221
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 1 88.2482 110.265 1.24949
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted 204.641 161.051 43.59
102 60s ribosomal protein l18a. [swissprot;acc:q02543] Divided 0 12738.7 10437.1 1.22052
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted 1 204.642 161.068 43.574
importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 0 7168 5102 2066
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Divided 1 88.2482 110.265 1.24949
103 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 0 7495.26 9130.38 1.21815
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] Subtracted 18809.5 16764.2 2045.3
transcription factor jun-b. [swissprot;acc:p17275] 1 201.144 158.868 42.276
trophinin. [swissprot;acc:q12816] Divided 88.2482 110.265 1.24949
104 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 252.371 202.016 1.24926
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 0 9545 7868 1.21314
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] Subtracted 18809.5 16764.2 2045.3
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 1 256.228 298.438 42.21
105 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] Divided 0 17410.5 14360 1.21243
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 1 266.716 333.165 1.24914
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Subtracted 0 11853.5 9808.86 2044.64
transcription factor jun-d. [swissprot;acc:p17535] 1 200.941 158.941 42
106 brain protein 16. [refseq;acc:nm_016458] 0 6890.54 4854.99 2035.55
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Divided 16290.7 13464.8 1.20987
nostrin. [refseq;acc:nm_052946] Subtracted 1 209.299 249.187 39.888
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided 252.329 202.004 1.24913
107 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Subtracted 0 9183.49 11217.7 2034.21
eap30 subunit of ell complex. [refseq;acc:nm_007241] 1 209.299 249.187 39.888
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Divided 252.309 201.998 1.24907
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] 0 11853.5 9808.86 1.20845
108 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Subtracted 6742.5 8759.5 2017
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Divided 1 252.296 201.995 1.24902
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Subtracted 209.299 249.187 39.888
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Divided 0 10585.3 12769.1 1.2063
109 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 14466.8 12031.7 1.20239
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Subtracted 1 209.299 249.187 39.888
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Divided 266.933 333.281 1.24856
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Subtracted 0 9940.69 11929 1988.31
110 deltex 2. [refseq;acc:nm_020892] Divided 1 333.144 267.393 1.2459
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 0 12584.5 10470.6 1.20189
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Subtracted 1 209.299 249.187 39.888
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 0 14864.7 16820.7 1956
111 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Divided 1 332.925 267.274 1.24563
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Subtracted 209.299 249.187 39.888
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Divided 0 9940.69 11929 1.20002
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] Subtracted 13255.4 15183.2 1927.8
112 40s ribosomal protein s26. [swissprot;acc:p02383] Divided 14269.7 17098 1.1982
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Subtracted 1 275.754 235.908 39.846
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 0 8335.82 10228.3 1892.48
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] Divided 1 332.874 267.246 1.24557
113 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Subtracted 0 8335.82 10228.3 1892.48

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/