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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Gene Filtered Rank green description Network Comparison Type Value Type Interaction Map network_comparison red
Results: HTML CSV LaTeX Showing element 101 to 150 of 9634 in total
Filtered  : 0
Network Comparison Type  : Divided
Value Type  : Ranked
Rank
green
description
Interaction Map
network_comparison
red
51 5102 importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] High confidence 1.40494 7168
9346.75 succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Low confidence 1.30983 12242.7
52 4554.5 ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] High confidence 1.38688 3284
5406 rna transcribed from l1 repetitive element (shr4) (fragment). [sptrembl;acc:q9y443] Low confidence 1.30744 7068
53 4554.5 ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] High confidence 1.38688 3284
5406 putative p150. [sptrembl;acc:o00370] Low confidence 1.30744 7068
54 lamin-like protein in hindiii repetitive element derived dna, 3' end (fragment). [sptrembl;acc:q14755]
19014.6 syntaxin 10 (syn10). [swissprot;acc:o60499] High confidence 1.36949 13884.4
55 5406 line-1 reverse transcriptase (fragment). [sptrembl;acc:o00172] Low confidence 1.30744 7068
16388 sedlin. [swissprot;acc:o14582] High confidence 1.36929 22440
56 13931.4 phosphatase and tensin homolog 2 (fragment). [sptrembl;acc:o43460] Low confidence 1.30665 18203.5
16388 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] High confidence 1.36929 22440
57 7869.25 testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Low confidence 1.30622 10279
11134.8 hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] High confidence 1.36581 8152.55
58 14294.6 fos39347_1. [sptrembl;acc:o75863] Low confidence 1.29661 11024.6
14486 dead-box protein. [refseq;acc:nm_018665] High confidence 1.36296 10628.3
59 11662.3 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 1.36025 15863.6
14282.8 dj254p11.1 (novel protein similar to rna polymerase ii elongation factor siii, subunit p15). [sptrembl;acc:q9h575] Low confidence 1.29479 11031
60 14378 ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760] 1.29392 18604
15924 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] High confidence 1.35397 11761
61 10324.5 protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Low confidence 1.29018 13320.5
11346.5 testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] High confidence 1.35302 15352
62 6438 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Low confidence 1.28017 5029
12695.6 glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] High confidence 1.34791 9418.7
63 11453 oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 1.34428 8519.83
15783.5 60s ribosomal protein l37a. [swissprot;acc:p12751] Low confidence 1.27551 12374.3
64 11356 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 1.2736 14463
20387 similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] High confidence 1.33563 15264
65 10406.3 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 1.32502 7853.67
12943.5 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Low confidence 1.27245 10172.1
66 10030.4 kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 1.26584 7923.89
15180 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] High confidence 1.32449 11461
67 14291.5 presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 1.32408 10793.5
14697.6 dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] Low confidence 1.26309 11636.2
68 9824.6 repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 1.25899 7803.58
11823.3 purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] High confidence 1.32362 8932.56
69 10174.1 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 1.32051 7704.7
12610.3 transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Low confidence 1.25855 15870.7
70 10593.2 protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] High confidence 1.31931 13975.7
12392 latrophilin 2; lectomedin-1; latrophilin homolog 2 (cow). [refseq;acc:nm_012302] Low confidence 1.25731 9856
71 5700.79 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] High confidence 1.31395 4338.65
9117 sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Low confidence 1.25575 11448.7
72 5397 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] High confidence 1.31027 4119
21866 carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615] Low confidence 1.25314 17449
73 5397 phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] High confidence 1.31027 4119
21866 carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] Low confidence 1.25314 17449
74 7386.89 oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 1.252 5900.08
8759.5 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] High confidence 1.29915 6742.5
75 11350 nanos (fragment). [sptrembl;acc:q8wy41] 1.29242 8782
12104.2 transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Low confidence 1.24934 9688.47

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/