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 451 to 500 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
57 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Subtracted Low confidence 0 13825.5 17020.5 3195
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] High confidence 1 185.678 245.247 59.569
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Divided Low confidence 202.802 182.73 1.10985
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Subtracted High confidence 0 19048 22389 3341
set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Low confidence 1 230.944 209.149 21.795
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Divided 0 10279 7869.25 1.30622
58 dead-box protein. [refseq;acc:nm_018665] High confidence 10628.3 14486 1.36296
fos39347_1. [sptrembl;acc:o75863] Low confidence 11024.6 14294.6 1.29661
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Subtracted High confidence 1 185.678 245.247 59.569
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided 266.863 336.191 1.25979
jun dimerization protein. [refseq;acc:nm_130469] Low confidence 202.802 182.73 1.10985
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Subtracted 0 13825.5 17020.5 3195
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 1 155.56 133.876 21.684
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] High confidence 0 12460.6 15781 3320.4
59 dj254p11.1 (novel protein similar to rna polymerase ii elongation factor siii, subunit p15). [sptrembl;acc:q9h575] Divided Low confidence 11031 14282.8 1.29479
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] High confidence 15863.6 11662.3 1.36025
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] Subtracted 9418.7 12695.6 3276.9
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Divided 1 266.863 336.19 1.25978
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted Low confidence 0 13825.5 17020.5 3195
mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] 1 221.902 200.783 21.119
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Divided 233.134 210.267 1.10875
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted High confidence 269.278 327.709 58.431
60 60s ribosomal protein l21. [swissprot;acc:p46778] 0 9994.33 6758.83 3235.5
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 1 269.254 327.655 58.401
ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760] Divided Low confidence 0 18604 14378 1.29392
fos-related antigen 2. [swissprot;acc:p15408] 1 202.793 182.961 1.10839
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] High confidence 0 11761 15924 1.35397
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 1 266.864 336.184 1.25976
malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] Subtracted Low confidence 211 231.635 20.635
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] 0 13825.5 17020.5 3195
61 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 1 229.144 208.803 20.341
cab2. [refseq;acc:nm_033419] 0 17615.9 14460.9 3155
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Divided High confidence 1 266.864 336.182 1.25975
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Subtracted 269.248 327.642 58.394
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Divided Low confidence 202.792 182.974 1.10831
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] 0 13320.5 10324.5 1.29018
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Subtracted High confidence 14463 11356 3107
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Divided 15352 11346.5 1.35302
62 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] Subtracted 17410.5 14360 3050.5
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Divided Low confidence 5029 6438 1.28017
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 1 202.79 183.017 1.10804
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] High confidence 0 9418.7 12695.6 1.34791
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1 266.865 336.181 1.25974
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Subtracted 269.23 327.601 58.371
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Low confidence 202.802 182.73 20.072
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 0 14463 11356 3107
63 60s ribosomal protein l37a. [swissprot;acc:p12751] Divided 12374.3 15783.5 1.27551
dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] Subtracted 11636.2 14697.6 3061.4
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided High confidence 1 266.865 336.178 1.25973
jun dimerization protein. [refseq;acc:nm_130469] Subtracted Low confidence 202.802 182.73 20.072

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/