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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2512 to 2561 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
628 Rooted serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 59.6661 64.3692 1.07882
629 Measured cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 6228.39 7013.19 1.126
Ranked gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 214.256 202.14 1.05994
Squared interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 32192.5 37966.8 1.17937
Rooted synapsin iii. [swissprot;acc:o14994] 60.0129 64.7371 1.07872
630 Measured disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] 6228.39 7013.19 1.126
Ranked nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 214.256 202.141 1.05993
Squared gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 32192.8 37967.1 1.17937
Rooted aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 60.0129 64.7371 1.07872
631 Measured kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] 6228.39 7013.19 1.126
Ranked similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 214.256 202.141 1.05993
Squared gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 32192.8 37967.1 1.17937
Rooted 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] 60.0129 64.7371 1.07872
632 Measured disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 6228.39 7013.19 1.126
Ranked homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 214.254 202.166 1.05979
Squared phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 32192.5 37966.8 1.17937
Rooted actin binding lim protein 2. [refseq;acc:nm_032432] 60.0129 64.7371 1.07872
633 Measured ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] 6228.39 7013.19 1.126
Ranked alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] 234.106 248.104 1.05979
Squared gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 32192.8 37967.2 1.17937
Rooted hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] 60.0129 64.7371 1.07872
634 Measured disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] 6228.39 7013.19 1.126
Ranked dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 226.523 213.786 1.05958
Squared gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 32192.8 37967.1 1.17937
Rooted synapsin ii. [swissprot;acc:q92777] 60.0129 64.7371 1.07872
635 Measured ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 6228.97 7013.53 1.12595
Ranked 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 228.639 242.258 1.05957
Squared homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 32189.9 37963.6 1.17936
Rooted mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] 60.0129 64.7371 1.07872
636 Measured proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] 5713.41 6432.92 1.12593
Ranked splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] 228.639 242.258 1.05957
Squared homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 32187.7 37961 1.17936
Rooted peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 60.0129 64.7371 1.07872
637 Measured putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 7756.51 8731.76 1.12573
Ranked amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] 228.639 242.258 1.05957
Squared homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 32188.2 37961.6 1.17936
Rooted hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] 60.0129 64.7371 1.07872
638 Measured nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] 7755.69 8730.74 1.12572
Ranked sorting nexin 17. [swissprot;acc:q15036] 228.639 242.258 1.05957
Squared homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 32183.5 37955.7 1.17935
Rooted transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] 60.0129 64.7371 1.07872
639 Measured nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] 7753.59 8728.13 1.12569
Ranked nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] 217.67 230.596 1.05938
Squared bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 17618.8 20776.8 1.17924
Rooted delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] 60.0129 64.7371 1.07872
640 Measured glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 4811.02 5414.64 1.12547
Ranked intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] 217.67 230.596 1.05938
Squared nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] 22848.5 26941.5 1.17914
Rooted actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] 60.0129 64.7371 1.07872
641 Measured peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] 4810.85 5414.21 1.12542

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/