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 9164 to 9213 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2291 inositol polyphosphate multikinase. [refseq;acc:nm_152230] Rooted 61.2156 62.4097 1.01951
2292 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6]
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Measured 5783.76 6048.94 1.04585
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Squared 27825.3 30004.3 1.07831
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Ranked 200.158 201.213 1.00527
2293 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] Rooted 61.2156 62.4097 1.01951
large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Ranked 200.158 201.213 1.00527
polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] Measured 5783.76 6048.94 1.04585
rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799] Squared 27825.3 30004.3 1.07831
2294 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] Measured 5783.73 6048.91 1.04585
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Ranked 162.331 163.187 1.00527
sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Squared 20777.7 22395 1.07784
spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] Rooted 59.3947 60.543 1.01933
2295 glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211] Measured 6066.61 6344.65 1.04583
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Squared 25799.2 27805.2 1.07775
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 1.01933
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Ranked 162.86 163.712 1.00523
2296 eyes absent homolog 4. [swissprot;acc:o95677] Measured 5784.9 6049.99 1.04582
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Rooted 59.3947 60.543 1.01933
phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] Ranked 206.451 205.38 1.00521
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Squared 26075.5 28102.3 1.07773
2297 dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] 27827.3 29985.3 1.07755
epsin 3. [refseq;acc:nm_017957] Ranked 218.153 219.284 1.00518
lamin a/c (70 kda lamin). [swissprot;acc:p02545] Rooted 62.3374 63.5406 1.0193
rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] Measured 6570.31 6871.29 1.04581
2298 centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] Rooted 62.3376 63.5406 1.0193
rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407] Measured 6570.74 6871.6 1.04579
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Squared 43485.2 40358.3 1.07748
ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068] Ranked 215.239 216.339 1.00511
2299 centaurin beta 2 (cnt-b2). [swissprot;acc:q15057] Rooted 62.3376 63.5406 1.0193
eyes absent homolog 2. [swissprot;acc:o00167] Measured 5786.15 6050.71 1.04572
p10-binding protein. [refseq;acc:nm_024491] Squared 25530 27505 1.07736
udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] Ranked 215.239 216.339 1.00511
2300 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 191.563 192.541
centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] Rooted 62.3376 63.5406 1.0193
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Squared 23187.6 24974.4 1.07706
rh type c glycoprotein. [refseq;acc:nm_016321] Measured 6573.3 6873.48 1.04567
2301 hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] 6946.6 7263.68 1.04565
lamin b1. [swissprot;acc:p20700] Rooted 62.3378 63.5405 1.01929
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Ranked 217.392 218.498 1.00509
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Squared 35770.9 38515.2 1.07672
2302 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] Measured 6946.6 7263.68 1.04565
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] Rooted 59.4004 60.5463 1.01929
hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] Ranked 191.567 192.542 1.00509
transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9] Squared 35770.9 38515.2 1.07672
2303 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] Ranked 191.567 192.542 1.00509
hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] Measured 6946.6 7263.68 1.04565
putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] Rooted 59.4004 60.5463 1.01929
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Squared 35770.9 38515.2 1.07672
2304 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] Measured 6946.38 7263.48 1.04565

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/