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 2651 to 2700 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
663 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Rooted 68.8197 74.1413 1.07733
tubby protein homolog. [swissprot;acc:p50607] Measured 6374.65 7145.59 1.12094
664 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Rooted 51.6042 55.574 1.07693
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 1.0577
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Measured 6374.65 7145.59 1.12094
ubiquitin-like protein smt3a. [swissprot;acc:p55854] Squared 23948 28164.1 1.17605
665 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] Ranked 229.072 216.576 1.0577
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Measured 6374.65 7145.59 1.12094
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Rooted 51.6042 55.574 1.07693
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Squared 18960.3 22298 1.17604
666 down-regulated in metastasis. [refseq;acc:nm_014503] Rooted 51.6042 55.574 1.07693
glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] Squared 29224 34362.1 1.17582
tbc1 domain family member 5. [swissprot;acc:q92609] Measured 6374.65 7145.59 1.12094
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Ranked 229.072 216.576 1.0577
667 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] Squared 29224 34362.1 1.17582
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Measured 6374.65 7145.59 1.12094
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Rooted 51.2483 47.5889 1.0769
668 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Ranked 229.072 216.576 1.0577
acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Rooted 95.4476 102.785 1.07687
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Squared 23969.3 28175.3 1.17547
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Measured 6374.65 7145.59 1.12094
669 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Rooted 79.931 86.0693 1.07679
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Measured 6374.65 7145.59 1.12094
synapsin i (brain protein 4.1). [swissprot;acc:p17600] Ranked 229.072 216.576 1.0577
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Squared 18548.7 21798.2 1.17519
670 autoantigen ngp-1. [swissprot;acc:q13823] Ranked 250.302 236.817 1.05694
dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Rooted 51.2122 47.5637 1.07671
dok-like protein. [refseq;acc:nm_024872] Squared 28911 33971.3 1.17503
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Measured 6374.65 7145.59 1.12094
671 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Squared 28911 33971.3 1.17503
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Ranked 210.739 199.398 1.05688
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Rooted 68.6822 73.8955 1.0759
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Measured 6374.65 7145.59 1.12094
672 dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Rooted 51.4203 47.7936 1.07588
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Squared 28911 33971.3 1.17503
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Ranked 210.739 199.398 1.05688
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Measured 6374.65 7145.59 1.12094
673 peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Ranked 226.497 214.355 1.05664
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Rooted 132.156 122.835 1.07588
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Measured 6933.17 7766.54 1.1202
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Squared 28911 33971.3 1.17503
674 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 42467.5 36156.7 1.17454
exocyst complex component sec5. [swissprot;acc:q96kp1] Rooted 132.114 122.802 1.07583
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Ranked 226.497 214.355 1.05664
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Measured 5549.2 6215.42 1.12006
675 poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Rooted 132.063 122.761 1.07577
single-minded homolog 1. [swissprot;acc:p81133] Ranked 226.497 214.355 1.05664
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Measured 5549.2 6215.42 1.12006
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Squared 22347.6 26247.3 1.1745

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/