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 373 to 422 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
94 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Subtracted 1 249.663 298.263 48.6
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 0 14222.5 12058.6 2163.9
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 1 88.2482 110.265 1.24949
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 0 12946.3 10519.7 1.23067
95 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 1 88.2482 110.265 1.24949
pp3111 protein. [refseq;acc:nm_022156] 0 6185 7603 1.22926
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Subtracted 1 249.663 298.263 48.6
zinc finger protein 232. [swissprot;acc:q9uny5] 0 11523.7 13686.9 2163.2
96 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 1 201.949 153.671 48.278
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Divided 0 8335.82 10228.3 1.22703
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 1 88.2482 110.265 1.24949
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Subtracted 0 11523 13685.4 2162.4
97 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] 1 271.752 225.68 46.072
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Divided 88.2482 110.265 1.24949
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 0 8335.82 10228.3 1.22703
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Subtracted 11522.8 13684.9 2162.1
98 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Divided 1 88.2482 110.265 1.24949
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] 0 7234.6 8858.94 1.22452
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Subtracted 1 204.641 160.957 43.684
zinc finger imprinted 2. [swissprot;acc:q9nzv7] 0 11520.7 13680.4 2159.7
99 jun dimerization protein. [refseq;acc:nm_130469] 1 204.641 160.957 43.684
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 88.2482 110.265 1.24949
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 0 12787.8 10454.7 1.22316
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Subtracted 7584.72 9706.12 2121.4
100 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Divided 9183.49 11217.7 1.22151
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Subtracted 12584.5 10470.6 2113.9
fos-related antigen 2. [swissprot;acc:p15408] 1 204.641 161.046 43.595
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 88.2482 110.265 1.24949
101 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Subtracted 0 12577.8 14662.1 2084.3
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Divided 14548.5 11915.2 1.221
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 1 88.2482 110.265 1.24949
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted 204.641 161.051 43.59
102 60s ribosomal protein l18a. [swissprot;acc:q02543] Divided 0 12738.7 10437.1 1.22052
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted 1 204.642 161.068 43.574
importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 0 7168 5102 2066
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] Divided 1 88.2482 110.265 1.24949
103 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 0 7495.26 9130.38 1.21815
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] Subtracted 18809.5 16764.2 2045.3
transcription factor jun-b. [swissprot;acc:p17275] 1 201.144 158.868 42.276
trophinin. [swissprot;acc:q12816] Divided 88.2482 110.265 1.24949
104 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 252.371 202.016 1.24926
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 0 9545 7868 1.21314
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] Subtracted 18809.5 16764.2 2045.3
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 1 256.228 298.438 42.21
105 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] Divided 0 17410.5 14360 1.21243
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 1 266.716 333.165 1.24914
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Subtracted 0 11853.5 9808.86 2044.64
transcription factor jun-d. [swissprot;acc:p17535] 1 200.941 158.941 42
106 brain protein 16. [refseq;acc:nm_016458] 0 6890.54 4854.99 2035.55
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Divided 16290.7 13464.8 1.20987

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/