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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 5058 to 5107 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
633 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Ranked Divided 234.106 248.104 1.05979
brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Rooted Subtracted 50.7723 46.0607 4.7116
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured 5201.41 4479.76 721.65
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Divided 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
topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] Squared Subtracted 28068.5 32522.9 4454.4
634 acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Ranked Divided 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
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Measured Subtracted 5201.41 4479.76 721.65
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] Rooted 59.6678 64.3767 4.7089
synapsin i (brain protein 4.1). [swissprot;acc:p17600] Ranked 229.072 216.576 12.496
synapsin ii. [swissprot;acc:q92777] Rooted Divided 60.0129 64.7371 1.07872
635 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] Ranked 228.639 242.258 1.05957
atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134] Squared Subtracted 28068.5 32522.9 4454.4
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Measured Divided 6228.97 7013.53 1.12595
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Squared 32189.9 37963.6 1.17936
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Measured Subtracted 5201.41 4479.76 721.65
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Ranked 235.296 247.673 12.377
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Rooted 50.5816 45.8738 4.7078
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Divided 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
probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] Squared Subtracted 28068.5 32522.9 4454.4
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Rooted 59.6674 64.3747 4.7073
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 Divided 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
thymic stromal co-transporter. [refseq;acc:nm_033051] Measured Subtracted 5201.41 4479.76 721.65
vav proto-oncogene. [swissprot;acc:p15498] Ranked 212.2 199.849 12.351
637 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] Divided 228.639 242.258 1.05957
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
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Measured Subtracted 4889.21 5610.52 721.31
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Rooted 59.6673 64.3742 4.7069
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Measured Divided 7756.51 8731.76 1.12573
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Squared Subtracted 35889.7 31448.5 4441.2
vav-3 protein. [swissprot;acc:q9ukw4] Ranked 212.253 199.908 12.345
638 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Squared Divided 32183.5 37955.7 1.17935
n-myc proto-oncogene protein. [swissprot;acc:p04198] Measured Subtracted 4889.71 5610.69 720.98
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] Divided 7755.69 8730.74 1.12572
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Squared Subtracted 22387.1 26827.3 4440.2
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Rooted 59.6661 64.3692 4.7031
sorting nexin 17. [swissprot;acc:q15036] Ranked Divided 228.639 242.258 1.05957
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Rooted 60.0129 64.7371 1.07872
vav-2 protein. [swissprot;acc:p52735] Ranked Subtracted 212.526 200.212 12.314
639 60s ribosomal protein l26. [swissprot;acc:q02877] Rooted 50.2549 45.5599 4.695
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] Squared Divided 17618.8 20776.8 1.17924
delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] Rooted 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
- 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/