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 686 to 735 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
43 nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Squared Divided 0 16.747 98.4675 5.87971
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Measured Subtracted 4089.65 4696.36 606.71
zinc finger protein 277. [swissprot;acc:q9nrm2] Rooted 90.4079 98.9265 8.5186
44 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] Measured Divided 45.4292 98.5074 2.16837
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Subtracted 1 28136.5 33457.6 5321.1
fos-related antigen 2. [swissprot;acc:p15408] Ranked Divided 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
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Rooted 0 11.9583 6.85565 1.7443
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Ranked Subtracted 15863.6 11662.3 4201.3
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Rooted Divided 1 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
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked Subtracted 332.874 267.246 65.628
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Squared 110342 184298 73956
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 77.7165 16.8473
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 0 33.5215 25.0836 8.4379
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Measured 2285.62 1681.3 604.32
serpin b12. [swissprot;acc:q96p63] Ranked Divided 14604.2 21138.6 1.44743
tigger transposable element derived 6. [refseq;acc:nm_030953] Squared 14.8773 83.3977 5.6057
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Subtracted 84448.4 89963.1 5514.7
45 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured 334.401 934.348 599.947
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted 24.4683 16.281 8.1873
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Divided 8.79142 14.7392 1.67654
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted 1 60.875 77.7152 16.8402
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Squared Divided 129597 73157.5 1.77148
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Ranked Subtracted 0 11761 15924 4163
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Measured Divided 1 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
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Ranked 0 14592 21113.7 1.44694
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Subtracted 1 332.874 267.246 65.628
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Squared 110342 184298 73956
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked Divided 204.641 161.051 1.27066
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Measured Subtracted 27642.5 22440.4 5202.1
tigger transposable element derived 6. [refseq;acc:nm_030953] Divided 0 202.374 438.605 2.1673
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Squared 14.8569 83.2781 5.60535
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Subtracted 25574.2 20063.8 5510.4
46 60s ribosomal protein l37a. [swissprot;acc:p12751] Ranked Divided 12941.7 18499.2 1.42943
apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared 1 129597 73157.5 1.77148
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Measured Subtracted 24896.4 20431.7 4464.7
deltex 2. [refseq;acc:nm_020892] Rooted Divided 27.634 43.9629 1.5909
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Squared Subtracted 0 30195 24837.5 5357.5
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked Divided 1 204.642 161.068 1.27053
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Subtracted 0 5210.5 9264.5 4054
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Rooted Divided 12.53 7.48331 1.67439
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Subtracted 25.1701 33.2721 8.102
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 1 137.446 120.823 16.623
neuralized-like. [refseq;acc:nm_004210] Ranked 332.326 266.948 65.378
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Measured Divided 779.167 1390.33 1.78438
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Squared Subtracted 210445 136779 73666
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Measured 0 3023.85 2436.4 587.45
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Squared Divided 14.8562 83.274 5.60534

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/