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 2463 to 2512 of 3228 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
green
network_comparison
2463 multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] 5114.15 5272.92 1.03105
2464 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] 6291.2 6486.07 1.03098
2465 germ cell-less. [refseq;acc:nm_022471] 7764.92 8003.67 1.03075
2466 pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] 7765.3 8004 1.03074
2467 pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426]
2468 hyporthetical protein mgc27169. [refseq;acc:nm_176782]
2469 homeobox protein meis1. [swissprot;acc:o00470]
2470 homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770]
2471 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816]
2472 pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425]
2473 pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245]
2474 homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687]
2475 zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] 3573.66 3682.14 1.03036
2476 zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] 3569.07 3676.7 1.03016
2477 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 3568.84 3676.43 1.03015
2478 zinc finger protein 232. [swissprot;acc:q9uny5] 3568.96 3676.57
2479 zinc finger protein 99. [refseq;acc:nm_032164] 3568.99 3676.6
2480 zinc finger protein 305. [swissprot;acc:o43309] 3568.95 3676.56
2481 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 3568.8 3676.39
2482 zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] 3568.99 3676.61
2483 zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] 3568.8 3676.38 1.03014
2484 zinc finger imprinted 2. [swissprot;acc:q9nzv7] 3568.45 3675.97 1.03013
2485 zinc finger protein 174 (aw-1). [swissprot;acc:q15697] 3568.18 3675.65 1.03012
2486 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 3626.38 3734.8 1.0299
2487 tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] 6963.12 7170.02 1.02971
2488 heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] 5637.59 5804.47 1.0296
2489 u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]
2490 glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] 6294.37 6472.9 1.02836
2491 hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] 3436.65 3531.96 1.02773
2492 growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257]
2493 growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]
2494 hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235]
2495 growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293]
2496 solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] 5534.46 5684.97 1.0272
2497 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] 7002.3 7192.25 1.02713
2498 helicase (fragment). [sptrembl;acc:q92771] 7002.03 7191.88 1.02711
2499 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] 8186.02 7971.27 1.02694
2500 rna polymerase i associated factor 53. [refseq;acc:nm_022490] 3804.53 3705.05 1.02685
2501 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 6562.71 6738.23 1.02675
2502 glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367]
2503 succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] 5996.06 6155.81 1.02664
2504 succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7]
2505 succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] 6237.83 6400.74 1.02612
2506 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 6200.39 6362.25 1.0261
2507 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] 4243.44 4352.56 1.02571
2508 lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] 6469.44 6634.31 1.02548
2509 reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] 6202.78 6360.79 1.02547
2510 succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] 6256.49 6415.21 1.02537
2511 integral membrane protein cii-3b. [sptrembl;acc:o75609] 6256.42 6415.04 1.02535
2512 reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] 6203.05 6360.18 1.02533

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/