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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Gene Rank description Value Type Network Comparison Type Filtered Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
description
Filtered
Interaction Map
green
red
network_comparison
113 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 1 High confidence 267.246 332.874 1.24557
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 0 6797.56 5673.33 1.19816
114 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 10603.2 8871.11 1.19525
disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] 1 Low confidence 211.983 197.779 1.07182
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence 267.246 332.874 1.24557
transcription factor tel-2 (ets-related protein tel2) (tel related ets factor). [swissprot;acc:q9y603] 0 Low confidence 9278.67 7730.67 1.20024
115 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] 1 211.983 197.779 1.07182
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] High confidence 267.246 332.874 1.24557
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 0 Low confidence 12255.4 10216.9 1.19952
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] High confidence 15627 18662.8 1.19427
116 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 1 334.483 268.565 1.24545
metaxin 1. [swissprot;acc:q13505] 0 16422.1 13761.3 1.19335
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Low confidence 6797.56 5673.33 1.19816
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] 1 190.791 204.161 1.07008
117 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 0 High confidence 13771.5 11545 1.19285
coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] 1 Low confidence 211.713 226.395 1.06935
neuralized-like. [refseq;acc:nm_004210] High confidence 266.948 332.326 1.24491
protein hspc134 (protein cda04). [swissprot;acc:q9by43] 0 Low confidence 13288.7 11114.8 1.19559
118 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] High confidence 14370.7 12049 1.19269
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Low confidence 9652.56 11535.2 1.19504
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 1 High confidence 228.934 284.753 1.24382
protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Low confidence 211.713 226.395 1.06935
119 cdc42-binding protein kinase beta; cdc42-binding protein kinase beta (dmpk-like); mrck beta; dmpk-like. [refseq;acc:nm_006035] 0 4873 5797 1.18962
mesoderm induction early response 1. [refseq;acc:nm_020948] High confidence 4302.5 3609 1.19216
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] 1 259.004 318.982 1.23157
natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Low confidence 211.107 225.666 1.06897
120 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence 327.709 269.278 1.21699
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 0 4873 5797 1.18962
Low confidence
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 1 189.965 203.016 1.0687
121 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 0 12636.7 10652.4 1.18628
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 1 High confidence 327.655 269.254 1.2169
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Low confidence 189.985 203.007 1.06854
zinc finger protein 232. [swissprot;acc:q9uny5] 0 High confidence 13686.9 11523.7 1.18772
122 hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Low confidence 10506.7 12458.3 1.18575
nanos (fragment). [sptrembl;acc:q8wy41] 1 217.479 203.66 1.06785
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] High confidence 327.642 269.248 1.21688
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 0 13685.4 11523 1.18766
123 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 1 327.601 269.23 1.21681
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] 0 Low confidence 13865.5 11725.7 1.18249
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 1 190.094 202.96 1.06768
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 0 High confidence 13684.9 11522.8 1.18764
124 high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 1 171.595 208.52 1.21519
natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Low confidence 210.566 224.763 1.06742
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 0 11039.5 9351.39 1.18052
zinc finger imprinted 2. [swissprot;acc:q9nzv7] High confidence 13680.4 11520.7 1.18746
125 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 1 Low confidence 227.616 213.243 1.0674
high-mobility group 20a. [refseq;acc:nm_018200] High confidence 171.778 208.588 1.21429
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 0 18578 22038 1.18624
small edrk-rich factor 1a. [swissprot;acc:o75920] Low confidence 5690.5 4824.5 1.1795

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/