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 Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 5908 to 5957 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
1477 transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Divided High confidence 215.328 211.267 1.01922
1478 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] 215.122 211.066
t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435] Low confidence 198.794 194.608 1.02151
thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Subtracted High confidence 205.817 209.851 4.034
zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] Low confidence 203.346 199.108 4.238
1479 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] High confidence 205.817 209.851 4.034
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Divided 228.469 232.855 1.0192
swi/snf-related matrix-associated actin-dependent regulator of chromatin a3; snf2-like 3; helicase-like transcription factor; dna-binding protein/plasminogen activator inhibitor-1 regulator; sucrose nonfermenting-like 3. [refseq;acc:nm_003071] Subtracted Low confidence 202.287 198.05 4.237
ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [swissprot;acc:q16763] Divided 198.794 194.608 1.02151
1480 cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] High confidence 218.664 214.55 1.01918
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Subtracted 213.251 209.264 3.987
retinoic acid receptor rxr-gamma. [swissprot;acc:p48443] Divided Low confidence 203.213 198.935 1.0215
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Subtracted 200.929 196.693 4.236
1481 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] High confidence 225.148 221.177 3.971
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Divided 208.432 204.516 1.01915
sr rich protein. [refseq;acc:nm_032870] Low confidence 204.229 199.931 1.0215
ubiquitously transcribed x chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the x chromosome). [swissprot;acc:o15550] Subtracted 200.93 196.694 4.236
1482 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] High confidence 225.148 221.177 3.971
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Divided 224.354 220.15 1.0191
pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Subtracted Low confidence 197.57 193.334 4.236
retinoic acid receptor rxr-beta. [swissprot;acc:p28702] Divided 203.213 198.936 1.0215
1483 cervical cancer 1 protooncogene protein p40; regulator of tp53. [refseq;acc:nm_015416] 204.229 199.931
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Subtracted 201.541 197.306 4.235
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Divided High confidence 198.927 202.726 1.0191
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Subtracted 228.419 232.376 3.957
1484 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] Divided 198.927 202.726 1.0191
aldehyde dehydrogenase x, mitochondrial precursor (ec 1.2.1.3) (aldh class 2). [swissprot;acc:p30837] Low confidence 205.089 209.494 1.02148
cytochrome c. [swissprot;acc:p00001] Subtracted High confidence 228.419 232.376 3.957
fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Low confidence 201.541 197.306 4.235
1485 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] 200.475 196.24
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] High confidence 228.419 232.376 3.957
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Divided 207.877 203.989 1.01906
rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960] Low confidence 205.448 201.131 1.02146
1486 heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Subtracted High confidence 228.419 232.376 3.957
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Divided 207.877 203.989 1.01906
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Low confidence 201.541 197.306 1.02146
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Subtracted 197.603 193.375 4.228
1487 c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] 203.321 199.093
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Divided 201.236 197.009 1.02146
fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] Subtracted High confidence 228.419 232.376 3.957
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Divided 207.877 203.989 1.01906
1488 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Subtracted Low confidence 201.236 197.009 4.227
fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Divided 201.541 197.306 1.02146
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] High confidence 207.877 203.989 1.01906
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Subtracted 228.419 232.376 3.957
1489 a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588] Low confidence 206.235 202.009 4.226
elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] High confidence 228.419 232.376 3.957
elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] Divided Low confidence 202.955 198.692 1.02146
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] High confidence 213.251 209.264 1.01905
1490 40s ribosomal protein s7 (s8). [swissprot;acc:p23821] Subtracted Low confidence 205.505 201.279 4.226

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/