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 3680 to 3729 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
920 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Subtracted High confidence 3761.59 4319.69 558.1
921 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Divided Low confidence 7363.79 7652.55 1.03921
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Subtracted 7229.1 7542.73 313.63
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] High confidence 3831.17 4388.74 557.57
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Divided 6324.31 6948.5 1.0987
922 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Subtracted 3893.85 4450.98 557.13
reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] Low confidence 8202.26 8515.65 313.39
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Divided High confidence 5511.2 6054.71 1.09862
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Low confidence 7987.95 8300.91 1.03918
923 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Subtracted 7280.59 7593.87 313.28
eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Divided High confidence 4057.54 4457.66 1.09861
glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Low confidence 8186.49 8506.98 1.03915
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Subtracted High confidence 3790.11 4346.98 556.87
924 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 10243.4 9686.82 556.58
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Divided 5406.5 5939.42 1.09857
syndecan-3 (synd3). [swissprot;acc:o75056] Low confidence 9050.12 9404.18 1.03912
zinc finger protein 183-like 1. [refseq;acc:nm_178861] Subtracted 7543.76 7857 313.24
925 grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] High confidence 4134.77 4691.24 556.47
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Low confidence 7582.84 7895.87 313.03
my016 protein. [sptrembl;acc:q9h3k6] Divided 8398.07 8726.39 1.03909
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] High confidence 5637.43 6193.07 1.09856
926 grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Subtracted 4134.77 4691.24 556.47
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Divided Low confidence 8051.79 8366.23 1.03905
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Subtracted 7987.95 8300.91 312.96
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Divided High confidence 5637.45 6193.08 1.09856
927 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] Low confidence 8005.86 8318.27 1.03902
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] High confidence 5638.64 6194.22 1.09853
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Subtracted Low confidence 8047.55 8360.5 312.95
swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077] High confidence 4134.77 4691.24 556.47
928 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Low confidence 7278.71 7591.58 312.87
cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Divided High confidence 5638.46 6194.04 1.09853
junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] Low confidence 8287.37 8610.75 1.03902
swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078] Subtracted High confidence 4134.77 4691.24 556.47
929 citrate synthase, mitochondrial precursor (ec 2.3.3.1). [swissprot;acc:o75390] Divided Low confidence 8070.54 8385.43 1.03902
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Subtracted 7948.13 8260.82 312.69
surfeit locus protein 1. [swissprot;acc:q15526] Divided High confidence 5638.46 6194.04 1.09853
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] Subtracted 4134.77 4691.24 556.47
930 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Divided 5638.65 6194.23 1.09853
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Low confidence 7928.24 8237.48 1.039
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Subtracted High confidence 6281.21 6837.61 556.4
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Low confidence 7948.13 8260.82 312.69
931 acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] Divided 7637.56 7935.35 1.03899
cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Subtracted High confidence 6281.21 6837.61 556.4
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Low confidence 7948.13 8260.82 312.69
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Divided High confidence 5638.59 6194.17 1.09853
932 acidic leucine-rich nuclear phosphoprotein 32 family member a (potent heat-stable protein phosphatase 2a inhibitor i1pp2a) (hla-dr associated protein i) (phapi) (acidic nuclear phosphoprotein pp32) (cerebellar leucine rich acidic nuclear protein). [swissprot;acc:p39687] Low confidence 7637.56 7935.35 1.03899
activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Subtracted High confidence 6281.21 6837.61 556.4
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Low confidence 8059.35 8371.9 312.55
cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Divided High confidence 5638.46 6194.04 1.09853
933 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Subtracted Low confidence 8358.82 8671.34 312.52

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/