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 2001 to 2050 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1001 laf-4 protein (lymphoid nuclear protein related to af4). [swissprot;acc:p51826] Low confidence 6995.47 7262.59 1.03818
lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] High confidence 5680.76 6220.45 1.095
1002 all1 fused gene from 5q31. [refseq;acc:nm_014423] Low confidence 6995.48 7262.6 1.03818
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] High confidence 5680.76 6220.45 1.095
1003 seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]
spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106] Low confidence 6998.01 7265 1.03815
1004 o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] High confidence 5391.64 5903.72 1.09498
sh3 domain-binding protein 5 (sh3 domain-binding protein that preferentially associates with btk). [swissprot;acc:o60239] Low confidence 7804.72 8102.42 1.03814
1005 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] High confidence 5780.34 6329.3 1.09497
peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Low confidence 8039.58 8345.65 1.03807
1006 gk001 protein. [refseq;acc:nm_020198] 8422.24 8742.91
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] High confidence 5707.73 6249.1 1.09485
1007 electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] Low confidence 8161.56 8472.15 1.03806
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] High confidence 5707.73 6249.1 1.09485
1008 senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Low confidence 6913.4 7176.31 1.03803
single-minded homolog 1. [swissprot;acc:p81133] High confidence 5707.73 6249.1 1.09485
1009 calponin h2, smooth muscle (neutral calponin). [swissprot;acc:q99439] Low confidence 8086.9 8394.45 1.03803
synapsin iii. [swissprot;acc:o14994] High confidence 5791.82 6340.86 1.0948
1010 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Low confidence 7733.46 8027.45 1.03802
1011 calponin h1, smooth muscle (basic calponin) (calponin 1). [swissprot;acc:p51911] 8087.01 8394.5
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] High confidence 5791.82 6340.86 1.0948
1012 actin binding lim protein 2. [refseq;acc:nm_032432]
calponin, acidic isoform (calponin 3). [swissprot;acc:q15417] Low confidence 8087 8394.49 1.03802
1013 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 7733.95 8028.03
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] High confidence 5791.82 6340.86 1.0948
1014 dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Low confidence 7878.21 8177.69 1.03801
synapsin ii. [swissprot;acc:q92777] High confidence 5791.82 6340.86 1.0948
1015 mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Low confidence 7877.17 8176.48 1.038
1016 alpha glucosidase ii alpha subunit; likely ortholog of mouse g2an alpha glucosidase 2, alpha neutral subunit. [refseq;acc:nm_014610] 8456.9 8778.27
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] High confidence 5791.82 6340.86 1.0948
1017 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]
lysine-deficient protein kinase 2; mitogen-activated protein kinase kinase kinase; serologically defined colon cancer antigen 43. [refseq;acc:nm_006648] Low confidence 7769.69 8064.74 1.03797
1018 protein kinase, lysine deficient 4; putative protein kinase wnk4. [refseq;acc:nm_032387]
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] High confidence 5791.82 6340.86 1.0948
1019 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Low confidence 7769.69 8064.74 1.03797
1020 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] High confidence 5791.82 6340.86 1.0948
protein kinase, lysine deficient 1; kinase deficient protein. [refseq;acc:nm_018979] Low confidence 7769.69 8064.74 1.03797
1021 exonuclease nef-sp. [refseq;acc:nm_030941]
synapsin i (brain protein 4.1). [swissprot;acc:p17600] High confidence 5791.82 6340.86 1.0948
1022 mitochondrial import inner membrane translocase subunit tim13 b. [swissprot;acc:q9y5l4] Low confidence 7877.5 8176.51 1.03796
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] High confidence 6435.94 7045.75 1.09475
1023 adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] Low confidence 7716.88 8009.78 1.03796
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] High confidence 6435.02 7044.65 1.09474
1024 26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998] Low confidence 8385.76 8703.92 1.03794
cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] High confidence 5706.5 6245.55 1.09446
1025 phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 5511.96 6031.95 1.09434
striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Low confidence 7445.04 7727.46 1.03793

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/