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 description Value Type Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 6456 in total
Value Type  : Measured
Filtered  : 1
Interaction Map  : High confidence
Rank
description
Network Comparison Type
red
green
network_comparison
501 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Divided 4682.87 4093.05 1.1441
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Subtracted 10725.6 9896.32 829.28
502 huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 10719 9891.08 827.92
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Divided 6913.6 7907.05 1.1437
503 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Subtracted 6920.69 7747.63 826.94
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Divided 15182.5 13277.9 1.14344
504 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Subtracted 6920.71 7747.65 826.94
enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Divided 10067.9 11511 1.14334
505 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Subtracted 6920.69 7747.63 826.94
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Divided 6856.71 7838.3 1.14316
506 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Subtracted 6920.69 7747.63 826.94
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Divided 3893.85 4450.98 1.14308
507 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Subtracted 6920.69 7747.63 826.94
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Divided 6875.08 7858.38 1.14302
508 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 7556.75 8636.87 1.14293
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Subtracted 6920.69 7747.63 826.94
509 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Divided 7551.8 8630.06 1.14278
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Subtracted 6920.67 7747.6 826.93
510 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] 7087.23 7911.25 824.02
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Divided 5975.11 6826.24 1.14245
511 nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Subtracted 6912.56 7735.12 822.56
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Divided 5975.11 6826.24 1.14245
512 alpha-nac protein. [sptrembl;acc:q9h009] Subtracted 6912.27 7734.68 822.41
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Divided 10807.4 12338.5 1.14167
513 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 7485.08 8543.66 1.14143
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Subtracted 6912.09 7734.41 822.32
514 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Divided 7477 8532.02 1.1411
di-ras2. [refseq;acc:nm_017594] Subtracted 6912.08 7734.39 822.31
515 transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Divided 3890.53 4439.07 1.14099
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Subtracted 5084.26 5904.1 819.84
516 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1153.5 339.5 814
n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Divided 4910.6 5600.61 1.14051
517 galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902]
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Subtracted 1153.5 339.5 814
518 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]
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Divided 4910.6 5600.61 1.14051
519 db83 protein. [swissprot;acc:p57088] Subtracted 1153.5 339.5 814
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Divided 9648.27 10994.9 1.13957
520 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 9642.22 10986.4 1.13941
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Subtracted 3858.52 4669.27 810.75
521 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 6143.52 6950.75 807.23
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Divided 5390.78 6142.07 1.13937
522 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Subtracted 6148.94 6955.76 806.82
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Divided 9634.98 10976.2 1.1392
523 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 10640.2 12117.8 1.13887
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Subtracted 5865.79 6671.23 805.44
524 aquaporin 5. [swissprot;acc:p55064] Divided 10640 12117.6 1.13887
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Subtracted 5206.9 6010.04 803.14
525 lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Divided 10639.8 12117.3 1.13887
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Subtracted 5207.03 6010.1 803.07

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/