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 Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 975 to 1024 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
488 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Divided 10872.4 12447 1.14483
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Subtracted 7105.27 7953.71 848.44
489 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 7101.95 7949.85 847.9
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Divided 5281.11 6044.61 1.14457
490 histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Subtracted 7101.94 7949.84 847.9
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Divided 15274.9 13346.9 1.14445
491 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] 5980.15 6843.48 1.14437
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Subtracted 7067.46 7909.27 841.81
492 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Divided 5979.94 6842.76 1.14429
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Subtracted 6167.93 7007.7 839.77
493 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Divided 5979.95 6842.78 1.14429
494 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 5979.93 6842.72 1.14428
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Subtracted 6167.93 7007.7 839.77
495 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903]
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Divided 10804.7 12363.6 1.14428
496 inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Subtracted 6167.93 7007.7 839.77
nostrin. [refseq;acc:nm_052946] Divided 4682.87 4093.05 1.1441
497 eap30 subunit of ell complex. [refseq;acc:nm_007241]
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Subtracted 4714.85 5554.38 839.53
498 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Divided 4682.87 4093.05 1.1441
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Subtracted 6933.17 7766.54 833.37
499 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Divided 4682.87 4093.05 1.1441
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Subtracted 6938.22 7770.65 832.43
500 gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Divided 4682.87 4093.05 1.1441
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Subtracted 10733.4 9902.6 830.8
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

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/