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 Value Type Network Comparison Type description Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 451 to 500 of 19268 in total
Value Type  : Ranked
Rank
Network Comparison Type
description
Interaction Map
Filtered
red
network_comparison
green
57 Divided proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Low confidence 1 202.802 1.10985 182.73
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] 0 10279 1.30622 7869.25
Subtracted melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 13825.5 3195 17020.5
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] High confidence 1 185.678 59.569 245.247
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0 19048 3341 22389
set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Low confidence 1 230.944 21.795 209.149
58 Divided dead-box protein. [refseq;acc:nm_018665] High confidence 0 10628.3 1.36296 14486
fos39347_1. [sptrembl;acc:o75863] Low confidence 11024.6 1.29661 14294.6
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] High confidence 1 266.863 1.25979 336.191
jun dimerization protein. [refseq;acc:nm_130469] Low confidence 202.802 1.10985 182.73
Subtracted glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] High confidence 185.678 59.569 245.247
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Low confidence 0 13825.5 3195 17020.5
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 1 155.56 21.684 133.876
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] High confidence 0 12460.6 3320.4 15781
59 Divided dj254p11.1 (novel protein similar to rna polymerase ii elongation factor siii, subunit p15). [sptrembl;acc:q9h575] Low confidence 11031 1.29479 14282.8
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] High confidence 15863.6 1.36025 11662.3
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 1 266.863 1.25978 336.19
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] Low confidence 233.134 1.10875 210.267
Subtracted glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] High confidence 0 9418.7 3276.9 12695.6
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Low confidence 13825.5 3195 17020.5
mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] 1 221.902 21.119 200.783
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence 269.278 58.431 327.709
60 Divided ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760] Low confidence 0 18604 1.29392 14378
fos-related antigen 2. [swissprot;acc:p15408] 1 202.793 1.10839 182.961
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] High confidence 0 11761 1.35397 15924
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 1 266.864 1.25976 336.184
Subtracted 60s ribosomal protein l21. [swissprot;acc:p46778] 0 9994.33 3235.5 6758.83
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 1 269.254 58.401 327.655
malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] Low confidence 211 20.635 231.635
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 3195 17020.5
61 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] High confidence 1 266.864 1.25975 336.182
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Low confidence 202.792 1.10831 182.974
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] 0 13320.5 1.29018 10324.5
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] High confidence 15352 1.35302 11346.5
Subtracted 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] Low confidence 1 229.144 20.341 208.803
cab2. [refseq;acc:nm_033419] 0 17615.9 3155 14460.9
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] High confidence 1 269.248 58.394 327.642
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 0 14463 3107 11356
62 Divided ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Low confidence 5029 1.28017 6438
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 1 202.79 1.10804 183.017
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] High confidence 0 9418.7 1.34791 12695.6
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1 266.865 1.25974 336.181
Subtracted 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] 0 17410.5 3050.5 14360
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 1 269.23 58.371 327.601
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Low confidence 202.802 20.072 182.73
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 0 14463 3107 11356
63 Divided 60s ribosomal protein l37a. [swissprot;acc:p12751] 12374.3 1.27551 15783.5
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] High confidence 1 266.865 1.25973 336.178
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 0 8519.83 1.34428 11453
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Low confidence 1 265.688 1.10749 239.902

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/