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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2500 to 2549 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
625 HTRA2 Rooted serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] 59.6678 64.3767 1.07892
626 AHCYL1 Measured putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 6228.39 7013.19 1.126
GABRA2 Squared gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 32192.8 37967.1 1.17937
GABRE Ranked gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 214.256 202.14 1.05994
HTRA3 Rooted probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 59.6673 64.3742 1.07889
627 GABRA6 Squared gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 32192.8 37967.1 1.17937
HTRA4 Rooted probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 59.6674 64.3747 1.07889
JMJD6 Ranked phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 214.256 202.139 1.05994
KIAA0430 Measured limkain b1. [refseq;acc:nm_019081] 6228.39 7013.19 1.126
628 no value putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]
GABRA1 Ranked gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 214.256 202.14 1.05994
GABRG2 Squared gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 32192.6 37966.9 1.17937
HTRA1 Rooted serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 59.6661 64.3692 1.07882
629 no value Squared interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 32192.5 37966.8 1.17937
CREG1 Measured cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 6228.39 7013.19 1.126
GABRA3 Ranked gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 214.256 202.14 1.05994
SYN3 Rooted synapsin iii. [swissprot;acc:o14994] 60.0129 64.7371 1.07872
630 no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
DLGAP3 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
GABRA4 Squared gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 32192.8 37967.1 1.17937
NDUFA6 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
631 GABRE Squared gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 32192.8 37967.1 1.17937
HEY1 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
KNG1 Measured kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] 6228.39 7013.19 1.126
PDXDC1 Ranked similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 214.256 202.141 1.05993
632 no value 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
ABLIM2 Rooted actin binding lim protein 2. [refseq;acc:nm_032432] 60.0129 64.7371 1.07872
HOXD9 Ranked homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 214.254 202.166 1.05979
JMJD6 Squared phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 32192.5 37966.8 1.17937
633 AARS Ranked alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] 234.106 248.104 1.05979
FTL Measured ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] 6228.39 7013.19 1.126
GABRA1 Squared gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 32192.8 37967.2 1.17937
HEYL Rooted hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] 60.0129 64.7371 1.07872
634 no value Ranked dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 226.523 213.786 1.05958
DLGAP4 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
GABRA3 Squared gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 32192.8 37967.1 1.17937
SYN2 Rooted synapsin ii. [swissprot;acc:q92777] 60.0129 64.7371 1.07872
635 FTHL17 Measured ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 6228.97 7013.53 1.12595
HOXC9 Squared homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 32189.9 37963.6 1.17936
MRRF Rooted mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] 60.0129 64.7371 1.07872
RPL37 Ranked 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 228.639 242.258 1.05957
636 HOXB9 Squared homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 32187.7 37961 1.17936
PEX5 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
PSMA5 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
SFRS1 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
637 HEY2 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
HOXA9 Squared homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 32188.2 37961.6 1.17936
NME2P1 Measured putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 7756.51 8731.76 1.12573
PPAT Ranked amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] 228.639 242.258 1.05957
638 HES1 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

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
- Hugo is the HGNC identifier if it exists
- 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/