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 4008 to 4057 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2004 transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Divided 5047.87 5344.95 1.05885
2005 atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] 6064.92 6421.65 1.05882
scribble. [refseq;acc:nm_015356] Subtracted 5516.89 5844.37 327.48
2006 lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214] 5517.24 5844.68 327.44
transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] Divided 5048.26 5345.1 1.0588
2007 adaptor-related protein complex 1, mu 1 subunit (mu-adaptin 1) (adaptor protein complex ap-1 mu-1 subunit) (golgi adaptor ha1/ap1 adaptin mu-1 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 1) (clathrin coat assembly protein ap47) (clathrin coat associated protein ap47) (ap-mu chain family member mu1a). [swissprot;acc:q9bxs5] 5684.61 6018.72 1.05877
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Subtracted 4980.54 5307.81 327.27
2008 40s ribosomal protein s15a. [swissprot;acc:p39027] Divided 3637.47 3435.61 1.05876
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] Subtracted 4980.54 5307.81 327.27
2009 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Divided 4934.48 5223.69 1.05861
stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Subtracted 4980.54 5307.81 327.27
2010 adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] Divided 5671.62 6003.67 1.05855
stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] Subtracted 4980.54 5307.81 327.27
2011 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] Divided 5391.27 5706.64 1.0585
inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] Subtracted 5204.25 5530.11 325.86
2012 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Divided 5391.27 5706.64 1.0585
inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] Subtracted 5204.25 5530.11 325.86
2013 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9]
hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] Divided 5391.27 5706.64 1.0585
2014 ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Subtracted 5204.25 5530.11 325.86
kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] Divided 5934.08 6281.2 1.0585
2015 dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 6555.42 6938.82 1.05849
r3h domain protein 1. [swissprot;acc:q15032] Subtracted 5837.34 6162.91 325.57
2016 lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760] Divided 6555.42 6938.82 1.05849
proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618] Subtracted 6642.32 6967.61 325.29
2017 lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330] Divided 6555.42 6938.82 1.05849
uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Subtracted 5475.74 5800.97 325.23
2018 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]
mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Divided 6555.42 6938.82 1.05849
2019 inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] Subtracted 5475.74 5800.97 325.23
lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260] Divided 6555.42 6938.82 1.05849
2020 diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] 4935.84 5224.27 1.05844
uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] Subtracted 5475.74 5800.97 325.23
2021 kinesin-like protein kif3c. [swissprot;acc:o14782] Divided 5934.68 6281.49 1.05844
myosin vi. [swissprot;acc:q9um54] Subtracted 5475.74 5800.97 325.23
2022 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 8265.85 7940.87 324.98
enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Divided 5520.26 5841.16 1.05813
2023 lamin a/c (70 kda lamin). [swissprot;acc:p02545] Subtracted 5976.96 6301.73 324.77
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Divided 3560.24 3364.84 1.05807
2024 baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] 5976.81 6323.87
centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] Subtracted 5977.03 6301.76 324.73
2025 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] Divided 4813.13 5091.36 1.05781
centaurin beta 2 (cnt-b2). [swissprot;acc:q15057] Subtracted 5977.03 6301.76 324.73
2026 aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] Divided 6766.45 7155.54 1.0575
centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] Subtracted 5977.03 6301.76 324.73
2027 lamin b1. [swissprot;acc:p20700] 5977.09 6301.79 324.7
rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584] Divided 6218.34 6575.81 1.05749
2028 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 1.05746
presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352] Subtracted 5835.44 6159.45 324.01
2029 paraspeckle protein 1. [refseq;acc:nm_018282] Divided 10241.3 9685.21 1.05742

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/