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 4758 to 4807 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2379 serpin b11. [swissprot;acc:q96p15] Subtracted 5078.5 5275.76 197.26
2380 placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Divided 3690.79 3543.33 1.04162
2381 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Subtracted 5078.5 5275.76 197.26
dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Divided 3667.94 3521.41 1.04161
2382 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] 4457.6 4642.72 1.04153
leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Subtracted 5078.5 5275.76 197.26
2383 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Divided 4164.76 4337.01 1.04136
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Subtracted 3646.01 3449.54 196.47
2384 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Divided 4164.96 4336.92 1.04129
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Subtracted 3560.24 3364.84 195.4
2385 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Divided 3716.43 3569.68 1.04111
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Subtracted 8565.3 8760.3 195
2386 60s ribosomal protein l30. [swissprot;acc:p04645] Divided 3674.02 3529.35 1.04099
dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515] Subtracted 6291.2 6486.07 194.87
2387 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Divided 8265.85 7940.87 1.04092
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Subtracted 6042.36 6237.19 194.83
2388 60s ribosomal protein l26. [swissprot;acc:q02877] 3601.97 3409.48 192.49
diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Divided 4418.21 4594.87 1.03998
2389 60s ribosomal protein l35. [swissprot;acc:p42766] Subtracted 3602.25 3410.23 192.02
lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] Divided 6327.14 6579.38 1.03987
2390 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Subtracted 3602.75 3411.17 191.58
tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] Divided 6327.14 6579.38 1.03987
2391 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Subtracted 3602.75 3411.18 191.57
defender against cell death 1 (dad-1). [swissprot;acc:p46966] Divided 6327.14 6579.38 1.03987
2392 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Subtracted 3614.91 3423.89 191.02
t-complex 11. [refseq;acc:nm_018679] Divided 6327.14 6579.38 1.03987
2393 serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Subtracted 3614.91 3423.89 191.02
tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3] Divided 6327.14 6579.38 1.03987
2394 60s ribosomal protein l34. [swissprot;acc:p49207] Subtracted 3614.91 3423.89 191.02
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] Divided 5502.5 5721.43 1.03979
2395 homeobox protein otx2. [swissprot;acc:p32243] 5682 5905.08 1.03926
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Subtracted 3614.91 3423.89 191.02
2396 myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Divided 6711.27 6974.49 1.03922
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Subtracted 3614.91 3423.89 191.02
2397 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 3672.49 3482.34 190.15
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Divided 6707.29 6970.07 1.03918
2398 brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Subtracted 3672.49 3482.34 190.15
hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775] Divided 6707.29 6970.07 1.03918
2399 dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] Subtracted 7002.3 7192.25 189.95
homeobox protein otx1. [swissprot;acc:p32242] Divided 5691.1 5913.92 1.03915
2400 helicase (fragment). [sptrembl;acc:q92771] Subtracted 7002.03 7191.88 189.85
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Divided 4368.44 4539.34 1.03912
2401 60s ribosomal protein l19. [swissprot;acc:p14118] Subtracted 3687.49 3499.2 188.29
cone-rod homeobox protein. [swissprot;acc:o43186] Divided 5694.04 5916.78 1.03912
2402 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 5078.5 5275.76 1.03884
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Subtracted 5978.83 6166.89 188.06
2403 40s ribosomal protein s21. [swissprot;acc:p35265] Divided 5078.5 5275.76 1.03884
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Subtracted 5978.83 6166.89 188.06
2404 60s ribosomal protein l3-like. [swissprot;acc:q92901] 3617.81 3430.31 187.5

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/