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 18720 to 18769 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2340 wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] Rooted Divided 67.7017 68.9415 1.01831
2341 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] Ranked Subtracted 194.825 195.787 0.962
activated p21cdc42hs kinase. [refseq;acc:nm_005781] Divided 229.258 230.294 1.00452
cone-rod homeobox protein. [swissprot;acc:o43186] Measured Subtracted 5694.04 5916.78 222.74
heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792] Divided 5606.66 5854.45 1.0442
ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] Rooted 61.917 63.0402 1.01814
sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] Squared Subtracted 25184.4 26642.6 1458.2
spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] Rooted 59.3947 60.543 1.1483
synapsin i (brain protein 4.1). [swissprot;acc:p17600] Squared Divided 28264.4 30386.4 1.07508
2342 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] Measured 7007.72 7317.15 1.04416
conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] Subtracted 6931.15 7152.73 221.58
dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] Rooted Divided 56.6812 55.6717 1.01813
mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Ranked 229.258 230.294 1.00452
pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] Squared 26263.5 28227.6 1.07478
sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] Subtracted 25184.6 26642.8 1458.2
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Ranked 194.834 195.794 0.96
spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] Rooted 59.3947 60.543 1.1483
2343 40s ribosomal protein s5. [swissprot;acc:p46782] Measured Divided 3672.17 3516.98 1.04413
clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Squared Subtracted 25184.5 26642.7 1458.2
deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] Rooted Divided 53.2692 52.3236 1.01807
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Ranked 212.222 211.27 1.00451
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Rooted Subtracted 59.3947 60.543 1.1483
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Measured 6737.15 6957.34 220.19
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Ranked 194.834 195.794 0.96
twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] Squared Divided 28067 30162.6 1.07466
2344 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694] Measured Subtracted 6737.15 6957.34 220.19
acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] Ranked 194.842 195.8 0.958
carboxypeptidase a5. [refseq;acc:nm_080385] Measured Divided 8353.97 8001.45 1.04406
eyes absent homolog 2. [swissprot;acc:o00167] Squared Subtracted 25194 26651.6 1457.6
insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] Rooted 71.4071 72.5539 1.1468
kccr13l. [refseq;acc:nm_139179] Ranked Divided 219.878 218.893 1.0045
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Squared 28067 30162.6 1.07466
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Rooted 53.2692 52.3236 1.01807
2345 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] Subtracted 59.4004 60.5463 1.1459
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] Squared Divided 31216.4 33543.2 1.07454
carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Measured 8353.97 8001.45 1.04406
dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609] Ranked 219.878 218.893 1.0045
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Subtracted 212.222 211.27 0.952
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Rooted Divided 53.2692 52.3236 1.01807
sorting nexin 1. [swissprot;acc:q13596] Squared Subtracted 25436.8 26889.4 1452.6
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] Measured 5502.5 5721.43 218.93
2346 eyes absent homolog 3. [swissprot;acc:q99504] Squared 25159.9 26608.4 1448.5
importin 4. [refseq;acc:nm_024658] Ranked 220.921 221.863 0.942
map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] Rooted Divided 53.2692 52.3236 1.01807
myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] Measured Subtracted 8695.15 8912.98 217.83
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Divided 8353.97 8001.45 1.04406
putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] Rooted Subtracted 59.4004 60.5463 1.1459
salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162] Squared Divided 31216.4 33543.2 1.07454
serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Ranked 217.057 218.03 1.00448
2347 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Measured Subtracted 8695.15 8912.98 217.83

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/