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 Value Type Gene description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 12864 to 12913 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
2714 Rooted dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 48.4125 48.4851 1.0015
2715 Measured huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] 5332.98 5351.72 1.00351
Ranked basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 216.018 215.903 1.00053
Squared fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] 36800.7 36312.3 1.01345
Rooted pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] 69.1013 69.1987 1.00141
2716 Measured mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8] 5332.98 5351.72 1.00351
Ranked salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162] 216.018 215.903 1.00053
Squared pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] 45034.4 44464 1.01283
Rooted 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] 69.1013 69.1987 1.00141
2717 Measured palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] 5603.24 5583.64 1.00351
Ranked microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] 216.521 216.634 1.00052
Squared pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] 45034.4 44464 1.01283
Rooted dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 66.3542 66.4417 1.00132
2718 Measured beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] 5603.24 5583.64 1.00351
Ranked histidine-rich membrane protein ke4. [swissprot;acc:q92504] 216.52 216.632 1.00052
Squared hyporthetical protein mgc27169. [refseq;acc:nm_176782] 45034.4 44464 1.01283
Rooted thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] 56.2206 56.2918 1.00127
2719 Measured syntaxin 16 (syn16). [swissprot;acc:o14662] 5603.24 5583.64 1.00351
Ranked microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] 216.52 216.632 1.00052
Squared homeobox protein meis1. [swissprot;acc:o00470] 45034.4 44464 1.01283
Rooted bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 59.4705 59.5398 1.00117
2720 Measured 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] 5603.24 5583.64 1.00351
Ranked microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] 216.52 216.633 1.00052
Squared homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] 45034.4 44464 1.01283
Rooted 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 58.3416 58.4068 1.00112
2721 Measured syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] 5603.24 5583.64 1.00351
Ranked bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 221.022 221.116 1.00043
Squared bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] 45034.4 44464 1.01283
Rooted block 23. [sptrembl;acc:q8nhw5] 58.3407 58.4056 1.00111
2722 Measured alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920] 5603.24 5583.64 1.00351
Ranked transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] 219.308 219.214 1.00043
Squared pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] 45034.4 44464 1.01283
Rooted similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 58.3343 58.3966 1.00107
2723 Measured adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] 5603.24 5583.64 1.00351
Ranked lamin b2. [swissprot;acc:q03252] 219.323 219.413 1.00041
Squared pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] 45034.4 44464 1.01283
Rooted succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] 64.3749 64.3084 1.00103
2724 Measured synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] 5603.24 5583.64 1.00351
Ranked heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] 221.053 220.963 1.00041
Squared homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] 45034.4 44464 1.01283
Rooted glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 67.416 67.4829 1.00099
2725 Measured syntaxin 1b. [swissprot;acc:q15531] 5603.24 5583.64 1.00351
Ranked doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] 216.496 216.569 1.00034
Squared germ cell-less. [refseq;acc:nm_022471] 45030.7 44461 1.01281
Rooted glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] 67.416 67.4829 1.00099
2726 Measured fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] 5332.98 5351.72 1.00351
Ranked rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873] 221.001 220.927 1.00033
Squared adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] 30233.2 29898.1 1.01121
Rooted serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] 66.27 66.332 1.00094
2727 Measured melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] 5603.24 5583.64 1.00351

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/