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 Value Type description 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
Value Type
description
red
green
network_comparison
663 Squared acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 23947.7 28163.9 1.17606
Rooted nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 68.8197 74.1413 1.07733
664 Measured protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] 6374.65 7145.59 1.12094
Ranked peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 229.072 216.576 1.0577
Squared ubiquitin-like protein smt3a. [swissprot;acc:p55854] 23948 28164.1 1.17605
Rooted neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 51.6042 55.574 1.07693
665 Measured numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] 6374.65 7145.59 1.12094
Ranked hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] 229.072 216.576 1.0577
Squared u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 18960.3 22298 1.17604
Rooted 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] 51.6042 55.574 1.07693
666 Measured tbc1 domain family member 5. [swissprot;acc:q92609] 6374.65 7145.59 1.12094
Ranked transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] 229.072 216.576 1.0577
Squared glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] 29224 34362.1 1.17582
Rooted down-regulated in metastasis. [refseq;acc:nm_014503] 51.6042 55.574 1.07693
667 Measured tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] 6374.65 7145.59 1.12094
Ranked delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] 229.072 216.576 1.0577
Squared proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] 29224 34362.1 1.17582
Rooted ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 51.2483 47.5889 1.0769
668 Measured vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] 6374.65 7145.59 1.12094
Ranked actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] 229.072 216.576 1.0577
Squared isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 23969.3 28175.3 1.17547
Rooted acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 95.4476 102.785 1.07687
669 Measured numb-like protein (numb-r). [swissprot;acc:q9y6r0] 6374.65 7145.59 1.12094
Ranked synapsin i (brain protein 4.1). [swissprot;acc:p17600] 229.072 216.576 1.0577
Squared u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 18548.7 21798.2 1.17519
Rooted hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 79.931 86.0693 1.07679
670 Measured tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] 6374.65 7145.59 1.12094
Ranked autoantigen ngp-1. [swissprot;acc:q13823] 250.302 236.817 1.05694
Squared dok-like protein. [refseq;acc:nm_024872] 28911 33971.3 1.17503
Rooted dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 51.2122 47.5637 1.07671
671 Measured vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] 6374.65 7145.59 1.12094
Ranked nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 210.739 199.398 1.05688
Squared docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 28911 33971.3 1.17503
Rooted proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] 68.6822 73.8955 1.0759
672 Measured protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] 6374.65 7145.59 1.12094
Ranked nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 210.739 199.398 1.05688
Squared docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 28911 33971.3 1.17503
Rooted dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] 51.4203 47.7936 1.07588
673 Measured transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 6933.17 7766.54 1.1202
Ranked peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 226.497 214.355 1.05664
Squared tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 28911 33971.3 1.17503
Rooted poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 132.156 122.835 1.07588
674 Measured sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 5549.2 6215.42 1.12006
Ranked hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] 226.497 214.355 1.05664
Squared apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 42467.5 36156.7 1.17454
Rooted exocyst complex component sec5. [swissprot;acc:q96kp1] 132.114 122.802 1.07583
675 Measured sprouty homolog 3 (spry-3). [swissprot;acc:o43610] 5549.2 6215.42 1.12006
Ranked single-minded homolog 1. [swissprot;acc:p81133] 226.497 214.355 1.05664
Squared [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] 22347.6 26247.3 1.1745
Rooted poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 132.063 122.761 1.07577

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/