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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 68 to 117 of 502 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 0
Rank
Hugo
description
red
green
network_comparison
68 no value purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 8932.56 11823.3 1.32362
69 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 7704.7 10174.1 1.32051
70 protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 13975.7 10593.2 1.31931
71 NUP43 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 4338.65 5700.79 1.31395
72 PGAM4 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 4119 5397 1.31027
73 no value 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]
74 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 6742.5 8759.5 1.29915
75 nanos (fragment). [sptrembl;acc:q8wy41] 8782 11350 1.29242
76 spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 3474 2695 1.28905
77 RCC1 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 8821.32 11366.5 1.28853
78 no value repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 7584.72 9706.12 1.27969
79 NXF5 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 9465.55 12106.5 1.27901
80 DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 9102.34 11617.9 1.27636
81 SEPHS2 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 14463 11356 1.2736
82 no value dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 7706.5 6058 1.27212
83 SNRPB small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] 18359.8 14447.8 1.27077
84 STX1A syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] 12460.6 15781 1.26647
85 TBL2 transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] 9688.47 12104.2 1.24934
86 no value high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] 5677.96 4546.87 1.24876
87 HMG1L1 dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] 5677.89 4547.43 1.24859
88 HMG1L10 high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] 5677.86 4547.66 1.24852
89 SP100 nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] 5677.58 4549.85 1.24786
90 HMG4L high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] 5677.45 4550.87 1.24755
91 BMP8A bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 13841.2 11127.5 1.24387
92 no value dok-like protein. [refseq;acc:nm_024872] 17571 21783 1.23971
93 PMS2 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 7739.47 9580.95 1.23793
94 TKTL1 transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 12946.3 10519.7 1.23067
95 DUS1L pp3111 protein. [refseq;acc:nm_022156] 6185 7603 1.22926
96 IMMP2L imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 8335.82 10228.3 1.22703
97 no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
98 NR2E1 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] 7234.6 8858.94 1.22452
99 ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 12787.8 10454.7 1.22316
100 no value creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 9183.49 11217.7 1.22151
101 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] 14548.5 11915.2 1.221
102 60s ribosomal protein l18a. [swissprot;acc:q02543] 12738.7 10437.1 1.22052
103 FMO3 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 7495.26 9130.38 1.21815
104 VBP1 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 9545 7868 1.21314
105 no value 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] 17410.5 14360 1.21243
106 TSFM elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 16290.7 13464.8 1.20987
107 ATP1A2 sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] 11853.5 9808.86 1.20845
108 PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 10585.3 12769.1 1.2063
109 CSMD1 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 14466.8 12031.7 1.20239
110 TOP2B dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 12584.5 10470.6 1.20189
111 no value protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] 9940.69 11929 1.20002
112 40s ribosomal protein s26. [swissprot;acc:p02383] 14269.7 17098 1.1982
113 DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 5673.33 6797.56 1.19816
114 no value bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 8871.11 10603.2 1.19525
115 spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 18662.8 15627 1.19427
116 MTX1 metaxin 1. [swissprot;acc:q13505] 13761.3 16422.1 1.19335
117 no value basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 11545 13771.5 1.19285

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
- Hugo is the HGNC identifier if it exists
- 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/