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 Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 762 to 811 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
191 Ranked filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 226.582 198.444 1.14179
Squared aquaporin 5. [swissprot;acc:p55064] 71388.5 96035.2 1.34525
Rooted pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 63.1192 72.584 1.14995
192 Measured a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 17757.5 14008 1.26767
Ranked musashi 2 isoform a. [refseq;acc:nm_138962] 227.491 199.458 1.14055
Squared aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 71387.4 96033.4 1.34524
Rooted splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 53.6107 61.5862 1.14877
193 Measured raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 17756.5 14007.3 1.26766
Ranked musashi 1. [refseq;acc:nm_002442] 227.491 199.458 1.14055
Squared lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] 71386.9 96032.5 1.34524
Rooted nostrin. [refseq;acc:nm_052946] 59.6399 51.9242 1.1486
194 Measured cyclin g2. [swissprot;acc:q16589] 17738.6 13995.7 1.26743
Ranked nuclear protein ukp68. [refseq;acc:nm_024824] 227.491 199.458 1.14055
Squared aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 71346.6 95965.1 1.34505
Rooted eap30 subunit of ell complex. [refseq;acc:nm_007241] 59.6399 51.9242 1.1486
195 Measured cyclin g1 (cyclin g). [swissprot;acc:p51959] 17738.5 13995.6 1.26743
Ranked huntingtin interacting protein c. [refseq;acc:nm_012272] 227.971 200.417 1.13748
Squared translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] 71062.4 95488.9 1.34373
Rooted liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 59.6399 51.9242 1.1486
196 Measured serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] 17738.5 13995.7 1.26742
Ranked forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 263.215 231.407 1.13745
Squared calsyntenin-1 precursor. [swissprot;acc:o94985] 71062.4 95488.9 1.34373
Rooted glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 59.6399 51.9242 1.1486
197 Measured serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] 17738.5 13995.7 1.26742
Ranked forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 263.215 231.407 1.13745
Squared 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] 71062.4 95488.9 1.34373
Rooted gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 59.6399 51.9242 1.1486
198 Measured b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 17710.9 13977.7 1.26708
Ranked forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 263.191 231.394 1.13741
Squared protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] 71062.2 95488.6 1.34373
Rooted glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 59.6399 51.9242 1.1486
199 Measured serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 4916.8 3888.18 1.26455
Ranked palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 242.735 276.059 1.13729
Squared thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] 71062.2 95488.6 1.34373
Rooted source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 61.2893 70.3856 1.14842
200 Measured crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 4808.79 6074.21 1.26315
Ranked egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 242.718 276.018 1.1372
Squared gk001 protein. [refseq;acc:nm_020198] 71062.2 95488.6 1.34373
Rooted oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 61.2893 70.3856 1.14842
201 Measured t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 4810.22 6075.04 1.26294
Ranked splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 240.133 211.382 1.13601
Squared calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 71033.4 95440.2 1.3436
Rooted dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 61.2893 70.3856 1.14842
202 Measured enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 4812.01 6076.09 1.26269
Ranked short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 201.478 228.784 1.13553
Squared calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 71030.1 95434.8 1.34358
Rooted splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 57.3527 65.7973 1.14724
203 Measured autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 11757.8 9352.11 1.25723
Ranked ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 201.515 228.752 1.13516
Squared hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 20988.2 15632.1 1.34263

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/