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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Gene Rank description green Filtered Value Type Interaction Map Network Comparison Type red network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 38536 in total
Network Comparison Type  : Divided
Rank
description
green
Filtered
Value Type
Interaction Map
red
network_comparison
35 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 907.564 1 Measured High confidence 1836.71 2.02378
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 5.80678 0 Rooted Low confidence 9.84765 1.69589
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 35.5 Measured 105.5 2.97183
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 0.355148 Squared 3.41692 9.62112
necdin. [swissprot;acc:q99608] 61881.5 1 82347.8 1.33073
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 4871.6 0 Ranked High confidence 3208.8 1.5182
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 204.309 1 260.532 1.27519
protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479] 16243 0 Low confidence 11808.5 1.37553
regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] 63.2347 1 Rooted 54.8296 1.15329
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 258.59 Ranked 297.273 1.14959
36 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 2.18581 0 Rooted High confidence 4.30525 1.96964
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 204.309 1 Ranked 260.532 1.27519
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] 8.01325 0 Squared 84.64 10.5625
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 64.217 1 Rooted Low confidence 55.7086 1.15273
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 14964 0 Ranked High confidence 22422 1.4984
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 24.369 1 Rooted 40.2805 1.65294
907.741 Measured 1836.76 2.02344
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 56 0 157 2.80357
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 5.80678 Rooted Low confidence 9.84765 1.69589
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 35.5 Measured 105.5 2.97183
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 0.355148 Squared 3.41692 9.62112
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 61881.5 1 82347.8 1.33073
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 192141 High confidence 106226 1.80879
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 7593.77 Measured Low confidence 6462.09 1.17513
sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] 9520.8 0 Ranked 13052.7 1.37097
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 258.33 1 296.837 1.14906
37 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 934.348 0 Measured High confidence 334.401 2.79409
1034.13 Squared 101.05 10.2338
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 217.843 1 Ranked Low confidence 250.244 1.14874
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 2582 0 High confidence 3859 1.49458
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 24.3691 1 Rooted 40.2805 1.65293
907.763 Measured 1836.76 2.02339
jun dimerization protein. [refseq;acc:nm_130469] 7593.77 Low confidence 6462.09 1.17513
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 0.355148 0 Squared 3.41692 9.62112
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 5.80678 Rooted 9.84765 1.69589
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 35.5 Measured 105.5 2.97183
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 61881.5 1 Squared 82347.8 1.33073
myotubularin related protein 8. [refseq;acc:nm_017677] 8993.6 0 Ranked 12302 1.36786
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 192141 1 Squared High confidence 106226 1.80879
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 253 Ranked 322 1.27273
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] 9.39626 0 Rooted 4.83477 1.94348
testis-specific protein tex28. [swissprot;acc:o15482] 59.166 1 Low confidence 51.7058 1.14428
38 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] 10771 0 Ranked High confidence 7230 1.48976
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 0.52284 Squared 4.84 9.25713
glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] 282.937 1 Ranked Low confidence 247.202 1.14456
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 24.3692 Rooted High confidence 40.2804 1.65292
907.774 Measured 1836.76 2.02337
melanoma antigen, family b, 6. [refseq;acc:nm_173523] 61881.5 Squared Low confidence 82347.8 1.33073
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 0.355148 0 3.41692 9.62112

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/