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 description Gene Value Type Interaction Map Network Comparison Type green Filtered red network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 3730 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
description
green
Filtered
red
network_comparison
51 importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 5102 0 7168 1.40494
spermatogenesis associated 6. [refseq;acc:nm_019073] 105 1 133 1.26667
52 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 4554.5 0 3284 1.38688
53 transcription factor jun-b. [swissprot;acc:p17275] 158.868 1 201.144 1.26611
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] 4554.5 0 3284 1.38688
54 syntaxin 10 (syn10). [swissprot;acc:o60499] 19014.6 13884.4 1.36949
transcription factor jun-d. [swissprot;acc:p17535] 158.941 1 200.941 1.26425
55 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 254.434 320.927 1.26134
sedlin. [swissprot;acc:o14582] 16388 0 22440 1.36929
56 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 336.233 1 266.856 1.25998
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 16388 0 22440 1.36929
57 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 336.233 1 266.856 1.25998
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 11134.8 0 8152.55 1.36581
58 dead-box protein. [refseq;acc:nm_018665] 14486 10628.3 1.36296
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 336.191 1 266.863 1.25979
59 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 11662.3 0 15863.6 1.36025
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 336.19 1 266.863 1.25978
60 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 15924 0 11761 1.35397
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 336.184 1 266.864 1.25976
61 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 336.182 1.25975
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] 11346.5 0 15352 1.35302
62 glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] 12695.6 9418.7 1.34791
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 336.181 1 266.865 1.25974
63 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 336.178 1.25973
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 11453 0 8519.83 1.34428
64 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 336.159 1 266.868 1.25965
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 20387 0 15264 1.33563
65 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 10406.3 7853.67 1.32502
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 336.077 1 267.136 1.25807
66 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 15180 0 11461 1.32449
67 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 336.075 1 267.14 1.25805
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 14291.5 0 10793.5 1.32408
68 guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 336.075 1 267.139 1.25805
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 11823.3 0 8932.56 1.32362
69 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 10174.1 7704.7 1.32051
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 336.075 1 267.14 1.25805
70 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] 336.074 267.142 1.25804
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 10593.2 0 13975.7 1.31931
71 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] 336.073 1 267.144 1.25802
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 5700.79 0 4338.65 1.31395
72 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] 336.073 1 267.144 1.25802
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 5397 0 4119 1.31027
73 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 362 1 288 1.25694
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] 5397 0 4119 1.31027
74 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 8759.5 6742.5 1.29915
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 362 1 288 1.25694
75 nanos (fragment). [sptrembl;acc:q8wy41] 11350 0 8782 1.29242
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 362 1 288 1.25694

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/