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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 12864 to 12913 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2714 similar to trna synthetase class ii. [refseq;acc:nm_152268] Ranked 220.224 220.348 1.00056
2715 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 216.018 215.903 1.00053
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Squared 36800.7 36312.3 1.01345
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Measured 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]
mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8] Measured 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
2717 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] Rooted 66.3542 66.4417 1.00132
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Ranked 216.521 216.634 1.00052
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Measured 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
2718 beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] Measured 5603.24 5583.64 1.00351
histidine-rich membrane protein ke4. [swissprot;acc:q92504] Ranked 216.52 216.632 1.00052
hyporthetical protein mgc27169. [refseq;acc:nm_176782] Squared 45034.4 44464 1.01283
thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] Rooted 56.2206 56.2918 1.00127
2719 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 59.4705 59.5398 1.00117
homeobox protein meis1. [swissprot;acc:o00470] Squared 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
homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] Squared 45034.4 44464 1.01283
microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] Ranked 216.52 216.633 1.00052
2721 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] Squared 45034.4 44464 1.01283
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] Ranked 221.022 221.116 1.00043
block 23. [sptrembl;acc:q8nhw5] Rooted 58.3407 58.4056 1.00111
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Measured 5603.24 5583.64 1.00351
2722 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] Squared 45034.4 44464 1.01283
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Rooted 58.3343 58.3966 1.00107
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Ranked 219.308 219.214 1.00043
2723 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] Measured 5603.24 5583.64 1.00351
lamin b2. [swissprot;acc:q03252] Ranked 219.323 219.413 1.00041
pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] Squared 45034.4 44464 1.01283
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Rooted 64.3749 64.3084 1.00103
2724 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 67.416 67.4829 1.00099
heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] Ranked 221.053 220.963 1.00041
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] Squared 45034.4 44464 1.01283
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 1.00351
2725 doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] Ranked 216.496 216.569 1.00034
germ cell-less. [refseq;acc:nm_022471] Squared 45030.7 44461 1.01281
glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] Rooted 67.416 67.4829 1.00099
syntaxin 1b. [swissprot;acc:q15531] Measured 5603.24 5583.64 1.00351
2726 adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] Squared 30233.2 29898.1 1.01121
fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Measured 5332.98 5351.72 1.00351
rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873] Ranked 221.001 220.927 1.00033
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] Rooted 66.27 66.332 1.00094
2727 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] Ranked 221.001 220.927 1.00033

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/