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 10714 to 10763 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
838 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] Measured Subtracted 6520.28 7119.28 599
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Squared Divided 31100.1 36086.4 1.16033
pbk1 protein. [sptrembl;acc:o76021] Measured 4064.23 4493.36 1.10559
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Rooted 65.0565 69.1533 1.06297
rw1 protein (fragment). [swissprot;acc:q92545] Ranked 231.734 222.222 1.0428
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Rooted Subtracted 81.454 85.4078 3.9538
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Squared 22328.1 26222.3 3894.2
839 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Measured Divided 7093.86 7842.67 1.10556
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Ranked Subtracted 230.764 239.62 8.856
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Squared Divided 31100.1 36086.4 1.16033
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Rooted 65.0565 69.1533 1.06297
proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] Measured Subtracted 6520.28 7119.28 599
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Ranked Divided 177.776 170.499 1.04268
target of myb protein 1. [swissprot;acc:o60784] Rooted Subtracted 61.6688 65.6175 3.9487
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Squared 22328.2 26222.4 3894.2
840 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 27235.1 31125.2 3890.1
deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] Ranked 236.741 245.547 8.806
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Measured 10300 9701.33 598.67
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] Rooted 61.6699 65.6173 3.9474
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Squared Divided 31100.1 36086.4 1.16033
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Ranked 198.781 190.66 1.04259
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Measured 5786.67 6395.78 1.10526
tbc1 domain family member 5. [swissprot;acc:q92609] Rooted 65.0565 69.1533 1.06297
841 conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Measured Subtracted 10300 9701.33 598.67
hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] Squared 27234.2 31123.3 3889.1
keratin associated protein 1.5. [refseq;acc:nm_031957] Divided 31100.2 36086.5 1.16033
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Measured 5786.67 6395.78 1.10526
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Ranked 198.781 190.66 1.04259
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Subtracted 236.741 245.547 8.806
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] Rooted 61.67 65.6173 3.9473
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Divided 65.0565 69.1533 1.06297
842 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] Squared Subtracted 27234.2 31123.3 3889.1
atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] Measured 5623.18 6218.77 595.59
jm1 protein. [refseq;acc:nm_014008] Ranked Divided 219.762 210.806 1.04248
loh1cr12. [refseq;acc:nm_058169] Measured 5195.48 5741.63 1.10512
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Ranked Subtracted 236.741 245.547 8.806
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Squared Divided 31100.1 36086.4 1.16033
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] Rooted Subtracted 61.6715 65.6171 3.9456
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Divided 65.0565 69.1533 1.06297
843 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] Measured Subtracted 5623.18 6218.77 595.59
hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] Squared 27234.2 31123.3 3889.1
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Divided 31100.2 36086.5 1.16033
map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] Ranked Subtracted 236.741 245.547 8.806
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Rooted Divided 65.0565 69.1533 1.06297
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Subtracted 59.6869 63.6262 3.9393
trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] Ranked Divided 218.521 227.796 1.04244
unr protein. [swissprot;acc:o75534] Measured 5195.48 5741.63 1.10512
844 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] Squared Subtracted 27233.3 31121.5 3888.2
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Measured 3641.89 4236.95 595.06
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Ranked Divided 178.033 170.82 1.04223

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/