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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2501 to 2550 of 12912 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
626 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Squared 32192.8 37967.1 1.17937
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Ranked 214.256 202.14 1.05994
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Rooted 59.6673 64.3742 1.07889
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Measured 6228.39 7013.19 1.126
627 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Squared 32192.8 37967.1 1.17937
limkain b1. [refseq;acc:nm_019081] Measured 6228.39 7013.19 1.126
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Ranked 214.256 202.139 1.05994
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Rooted 59.6674 64.3747 1.07889
628 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Ranked 214.256 202.14 1.05994
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Squared 32192.6 37966.9 1.17937
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Measured 6228.39 7013.19 1.126
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Rooted 59.6661 64.3692 1.07882
629 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Measured 6228.39 7013.19 1.126
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Ranked 214.256 202.14 1.05994
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Squared 32192.5 37966.8 1.17937
synapsin iii. [swissprot;acc:o14994] Rooted 60.0129 64.7371 1.07872
630 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Measured 6228.39 7013.19 1.126
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Squared 32192.8 37967.1 1.17937
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Ranked 214.256 202.141 1.05993
631 gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Squared 32192.8 37967.1 1.17937
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] Rooted 60.0129 64.7371 1.07872
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Measured 6228.39 7013.19 1.126
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Ranked 214.256 202.141 1.05993
632 actin binding lim protein 2. [refseq;acc:nm_032432] Rooted 60.0129 64.7371 1.07872
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Measured 6228.39 7013.19 1.126
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Ranked 214.254 202.166 1.05979
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Squared 32192.5 37966.8 1.17937
633 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Ranked 234.106 248.104 1.05979
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Measured 6228.39 7013.19 1.126
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Squared 32192.8 37967.2 1.17937
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Rooted 60.0129 64.7371 1.07872
634 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Ranked 226.523 213.786 1.05958
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Measured 6228.39 7013.19 1.126
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Squared 32192.8 37967.1 1.17937
synapsin ii. [swissprot;acc:q92777] Rooted 60.0129 64.7371 1.07872
635 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] Ranked 228.639 242.258 1.05957
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Measured 6228.97 7013.53 1.12595
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Squared 32189.9 37963.6 1.17936
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Rooted 60.0129 64.7371 1.07872
636 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Squared 32187.7 37961 1.17936
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Rooted 60.0129 64.7371 1.07872
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Measured 5713.41 6432.92 1.12593
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] Ranked 228.639 242.258 1.05957
637 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] Rooted 60.0129 64.7371 1.07872
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Squared 32188.2 37961.6 1.17936
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Measured 7756.51 8731.76 1.12573
638 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Squared 32183.5 37955.7 1.17935
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] Measured 7755.69 8730.74 1.12572

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/