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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
69 testis-specific protein tex28. [swissprot;acc:o15482] Divided Low confidence 1 259.517 235.017 1.10425
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 0 15870.7 12610.3 1.25855
70 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] 1 259.517 235.017 1.10425
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] High confidence 267.142 336.074 1.25804
latrophilin 2; lectomedin-1; latrophilin homolog 2 (cow). [refseq;acc:nm_012302] Low confidence 0 9856 12392 1.25731
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Subtracted High confidence 8082.33 5266.67 2815.66
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Low confidence 1 225.545 244.933 19.388
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Divided High confidence 0 13975.7 10593.2 1.31931
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Subtracted 1 188.688 242.742 54.054
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 0 12242.7 9346.75 2895.95
71 bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] High confidence 13841.2 11127.5 2713.7
cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Divided Low confidence 1 230.944 209.149 1.10421
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] High confidence 267.144 336.073 1.25802
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Subtracted 265.686 319.651 53.965
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Low confidence 0 8082.33 5266.67 2815.66
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Divided High confidence 4338.65 5700.79 1.31395
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 11448.7 9117 1.25575
transcription factor jun-d. [swissprot;acc:p17535] Subtracted 1 202.709 183.361 19.348
72 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 0 10172.1 12943.5 2771.4
carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615] Divided 17449 21866 1.25314
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] High confidence 1 267.144 336.073 1.25802
metaxin 1. [swissprot;acc:q13505] Subtracted 0 13761.3 16422.1 2660.8
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 1 265.639 319.546 53.907
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Divided 0 4119 5397 1.31027
set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Low confidence 1 230.944 209.149 1.10421
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Subtracted 227.623 208.281 19.342
73 carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] Divided 0 17449 21866 1.25314
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Subtracted 9282.29 6526.57 2755.72
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Divided High confidence 1 288 362 1.25694
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Subtracted 265.632 319.531 53.899
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 0 9465.55 12106.5 2640.95
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] Divided 4119 5397 1.31027
set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Low confidence 1 230.944 209.149 1.10421
transcription factor jun-b. [swissprot;acc:p17275] Subtracted 202.728 183.388 19.34
74 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Divided High confidence 0 6742.5 8759.5 1.29915
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Subtracted 14548.5 11915.2 2633.3
jumonji protein. [swissprot;acc:q92833] Low confidence 22296.2 19621 2675.2
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Divided High confidence 1 288 362 1.25694
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Low confidence 0 5900.08 7386.89 1.252
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Subtracted 1 225.428 244.701 19.273
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Divided 195.817 215.516 1.1006
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Subtracted High confidence 189.07 242.453 53.383
75 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 0 8158 5530.5 2627.5
bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] Low confidence 14899.4 17562.2 2662.8
nanos (fragment). [sptrembl;acc:q8wy41] Divided High confidence 8782 11350 1.29242
nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] Low confidence 1 249.709 226.944 1.10031
rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted 221.194 202.005 19.189
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] Divided High confidence 288 362 1.25694
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Low confidence 0 9688.47 12104.2 1.24934
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Subtracted High confidence 1 254.693 202.668 52.025

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/