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 25726 to 25775 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2714 inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Measured Divided 5603.24 5583.64 1.00351
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Rooted Subtracted 69.1013 69.1987 0.0974
similar to trna synthetase class ii. [refseq;acc:nm_152268] Ranked Divided 220.224 220.348 1.00056
2715 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] Rooted Subtracted 69.1013 69.1987 0.0974
adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] Measured 5603.24 5583.64 19.6
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] Ranked Divided 216.018 215.903 1.00053
Subtracted 0.115
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Squared Divided 36800.7 36312.3 1.01345
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Subtracted 2565.98 2308.67 257.31
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Measured Divided 5332.98 5351.72 1.00351
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Rooted 69.1013 69.1987 1.00141
2716 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]
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] Subtracted 66.3542 66.4417 0.0875
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Squared 2612.13 2364.75 247.38
mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8] Measured Divided 5332.98 5351.72 1.00351
pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] Squared 45034.4 44464 1.01283
salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162] Ranked 216.018 215.903 1.00053
Subtracted 0.115
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Measured 5603.24 5583.64 19.6
2717 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] Rooted Divided 66.3542 66.4417 1.00132
dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] Subtracted 48.4125 48.4851 0.0726
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Squared 2612.21 2364.84 247.37
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Ranked Divided 216.521 216.634 1.00052
Subtracted 0.113
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Measured Divided 5603.24 5583.64 1.00351
pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] Squared 45034.4 44464 1.01283
syntaxin 1b. [swissprot;acc:q15531] Measured Subtracted 5603.24 5583.64 19.6
2718 beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] Divided 1.00351
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Squared Subtracted 2612.98 2365.77 247.21
histidine-rich membrane protein ke4. [swissprot;acc:q92504] Ranked Divided 216.52 216.632 1.00052
hyporthetical protein mgc27169. [refseq;acc:nm_176782] Squared 45034.4 44464 1.01283
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Measured Subtracted 5603.24 5583.64 19.6
microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] Ranked 216.52 216.633 0.113
thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] Rooted Divided 56.2206 56.2918 1.00127
Subtracted 0.0712
2719 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] Divided 59.4705 59.5398 1.00117
Subtracted 0.0693
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Measured 5603.24 5583.64 19.6
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Squared 2613.08 2365.88 247.2
histidine-rich membrane protein ke4. [swissprot;acc:q92504] Ranked 216.52 216.632 0.112
homeobox protein meis1. [swissprot;acc:o00470] Squared Divided 45034.4 44464 1.01283
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] Ranked 216.52 216.632 1.00052
syntaxin 16 (syn16). [swissprot;acc:o14662] Measured 5603.24 5583.64 1.00351
2720 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] Rooted 58.3416 58.4068 1.00112
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Subtracted 78.2186 78.151 0.0676
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Measured 3953.53 3972.32 18.79
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Squared 2613.13 2365.94 247.19
homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] Divided 45034.4 44464 1.01283
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] Ranked Subtracted 216.52 216.632 0.112

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/