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 82 to 131 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
41 nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 0 266 645 2.42481
42 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] 1 1857.32 958.237 1.93827
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 0 205.439 86.9525 2.36266
43 elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 263.66 587.988 2.2301
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 1 1881.02 1027.36 1.83093
44 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] 0 45.4292 98.5074 2.16837
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 1 1931.34 1057.39 1.82652
45 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 1926.69 1056.02 1.82448
tigger transposable element derived 6. [refseq;acc:nm_030953] 0 202.374 438.605 2.1673
46 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 1 779.167 1390.33 1.78438
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] 0 202.163 438.035 2.16674
47 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 1 779.167 1390.33 1.78438
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] 0 202.156 438.016 2.16672
48 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 870.482 403.196 2.15895
doc-1 related protein (doc-1r). [swissprot;acc:o75956] 1 779.167 1390.33 1.78438
49 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 0 72 151 2.09722
50 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 1 779.167 1390.33 1.78438
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] 0 44 21 2.09524
51 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 1 779.167 1390.33 1.78438
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 0 184.422 88.5622 2.0824
52 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 1 779.167 1390.33 1.78438
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 0 999.28 481.725 2.07438
53 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 1 779.167 1390.33 1.78438
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 0 420.365 861.814 2.05016
54 deltex 2. [refseq;acc:nm_020892] 1 1618.84 2651.88 1.63814
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 0 638.862 330.189 1.93484
55 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 1 1629.21 2662.12 1.63399
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 0 630.942 327.517 1.92644
56 t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] 1 1631.67 2664.55 1.63302
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 0 271.484 142.981 1.89874
57 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 270.264 142.417 1.89769
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 1 1631.67 2664.55 1.63302
58 40s ribosomal protein s26. [swissprot;acc:p02383] 0 150.741 81.2233 1.85588
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1 1631.67 2664.55 1.63302
59 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 0 150.673 279.24 1.85328
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 1 1631.67 2664.55 1.63302
60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 4489.19 2765.82 1.6231
adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 0 47.4756 87.5499 1.8441
61 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 324.442 593.094 1.82804
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1 4489.19 2765.82 1.6231
62 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 0 210.767 384.407 1.82385
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1 4489.19 2765.82 1.6231
63 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 0 31.1429 56.278 1.80709
64 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1 4489.19 2765.82 1.6231
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 0 0.00001 18 1800000
65 neuralized-like. [refseq;acc:nm_004210] 1 1657.68 2690.25 1.6229
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0 18 0.00001 1800000
66 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 1 1991.03 3221.38 1.61795

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/