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 description Value Type Gene Network Comparison Type Interaction Map red green network_comparison Filtered
Results: HTML CSV LaTeX Showing element 551 to 600 of 38536 in total
Network Comparison Type  : Divided
Rank
description
Value Type
Interaction Map
red
green
network_comparison
Filtered
35 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Rooted High confidence 40.2812 24.3679 1.65304 1
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Low confidence 9.84765 5.80678 1.69589 0
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Measured 105.5 35.5 2.97183
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared 3.41692 0.355148 9.62112
necdin. [swissprot;acc:q99608] 82347.8 61881.5 1.33073 1
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Ranked High confidence 3208.8 4871.6 1.5182 0
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] 260.532 204.309 1.27519 1
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] Low confidence 11808.5 16243 1.37553 0
regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Rooted 54.8296 63.2347 1.15329 1
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Ranked 297.273 258.59 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] Rooted High confidence 4.30525 2.18581 1.96964 0
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] Ranked 260.532 204.309 1.27519 1
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Squared 84.64 8.01325 10.5625 0
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Rooted Low confidence 55.7086 64.217 1.15273 1
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] Ranked High confidence 22422 14964 1.4984 0
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Measured 1836.76 907.741 2.02344 1
Rooted 40.2805 24.369 1.65294
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Measured 157 56 2.80357 0
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Rooted Low confidence 9.84765 5.80678 1.69589
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Measured 105.5 35.5 2.97183
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared 3.41692 0.355148 9.62112
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 82347.8 61881.5 1.33073 1
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] High confidence 106226 192141 1.80879
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Measured Low confidence 6462.09 7593.77 1.17513
sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Ranked 13052.7 9520.8 1.37097 0
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 296.837 258.33 1.14906 1
37 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured High confidence 334.401 934.348 2.79409 0
Squared 101.05 1034.13 10.2338
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Ranked Low confidence 250.244 217.843 1.14874 1
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] High confidence 3859 2582 1.49458 0
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Measured 1836.76 907.763 2.02339 1
Rooted 40.2805 24.3691 1.65293
jun dimerization protein. [refseq;acc:nm_130469] Measured Low confidence 6462.09 7593.77 1.17513
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared 3.41692 0.355148 9.62112 0
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted 9.84765 5.80678 1.69589
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Measured 105.5 35.5 2.97183
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared 82347.8 61881.5 1.33073 1
myotubularin related protein 8. [refseq;acc:nm_017677] Ranked 12302 8993.6 1.36786 0
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Squared High confidence 106226 192141 1.80879 1
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Ranked 322 253 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] Rooted 4.83477 9.39626 1.94348 0
testis-specific protein tex28. [swissprot;acc:o15482] Low confidence 51.7058 59.166 1.14428 1
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] Ranked High confidence 7230 10771 1.48976 0
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Squared 4.84 0.52284 9.25713
glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] Ranked Low confidence 247.202 282.937 1.14456 1
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Measured High confidence 1836.76 907.774 2.02337
Rooted 40.2804 24.3692 1.65292
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Squared Low confidence 82347.8 61881.5 1.33073
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 3.41692 0.355148 9.62112 0

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/