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 Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5008 to 5057 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
626 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Measured Subtracted 8618.32 9340.98 722.66
627 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Squared Divided 32192.8 37967.1 1.17937
limkain b1. [refseq;acc:nm_019081] Measured 6228.39 7013.19 1.126
peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] Squared Subtracted 29881.4 34348 4466.6
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Ranked Divided 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
synapsin ii. [swissprot;acc:q92777] Ranked Subtracted 229.072 216.576 12.496
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Rooted 60.0129 64.7371 4.7242
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Measured 8618.32 9340.98 722.66
628 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] Rooted 60.0129 64.7371 4.7242
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Ranked Divided 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
j domain protein c21orf55. [swissprot;acc:q9nx36] Subtracted 58387.7 53925.7 4462
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Ranked 229.072 216.576 12.496
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Measured Divided 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
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Measured Subtracted 8618.32 9340.98 722.66
629 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Rooted 60.0129 64.7371 4.7242
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Measured Divided 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
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Measured Subtracted 5201.41 4479.76 721.65
peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] Squared 58385.9 53924.8 4461.1
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Ranked 229.072 216.576 12.496
synapsin iii. [swissprot;acc:o14994] Rooted Divided 60.0129 64.7371 1.07872
630 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Measured Subtracted 5201.41 4479.76 721.65
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Rooted Divided 60.0129 64.7371 1.07872
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
hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] Ranked Subtracted 229.072 216.576 12.496
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Divided 214.256 202.141 1.05993
prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675] Squared Subtracted 58385.9 53924.8 4461.1
synapsin i (brain protein 4.1). [swissprot;acc:p17600] Rooted 60.0129 64.7371 4.7242
631 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] 73.8577 78.5795 4.7218
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Measured 5201.41 4479.76 721.65
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Squared Divided 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
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Subtracted 229.072 216.576 12.496
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Squared 34152.7 38610.6 4457.9
632 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Rooted 50.7723 46.0607 4.7116
actin binding lim protein 2. [refseq;acc:nm_032432] Divided 60.0129 64.7371 1.07872
delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] Ranked Subtracted 229.072 216.576 12.496
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 Divided 6228.39 7013.19 1.126
ero1-like. [refseq;acc:nm_014584] Squared Subtracted 34152.7 38610.6 4457.9
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Ranked Divided 214.254 202.166 1.05979
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured Subtracted 5201.41 4479.76 721.65
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Squared Divided 32192.5 37966.8 1.17937
633 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Ranked Subtracted 229.072 216.576 12.496

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/