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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Gene description Rank Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1350 to 1399 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Rank
red
green
network_comparison
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 108 252.296 201.995 1.24902
homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [swissprot;acc:q15011] 3196 0.00001 0.00001 1
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 3053
homolog of yeast maf1. [refseq;acc:nm_032272] 1977 209.539 207.529 1.00969
hormone sensitive lipase (ec 3.1.1.-) (hsl). [swissprot;acc:q05469] 3172 0.00001 0.00001 1
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 289 272.781 246.892 1.10486
hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] 2231 221.842 223.246 1.00633
hsgcn1 (fragment). [sptrembl;acc:q99736] 2712 220.521 220.395 1.00057
hskin17 protein. [refseq;acc:nm_012311] 1697 217.624 214.69 1.01367
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 2258 223.888 225.191 1.00582
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] 1486 207.877 203.989 1.01906
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] 1488
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 1995 188.961 190.73 1.00936
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 1993 189.052 190.835 1.00943
huntingtin interacting protein c. [refseq;acc:nm_012272] 195 227.971 200.417 1.13748
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] 729 208.874 219.708 1.05187
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] 949 217.253 209.826 1.0354
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 179 226.884 194.79 1.16476
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 2415 218.2 218.984 1.00359
hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507] 2191 209.54 208.162 1.00662
hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282] 2192
hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] 1294 221.093 226.399 1.024
hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] 1291
hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] 1295
hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] 1104 231.922 238.486 1.0283
hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] 916 232.512 241.288 1.03774
hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775] 1640 194.516 197.364 1.01464
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 1648 219.745 222.928 1.01448
hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] 2304 191.567 192.542 1.00509
hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] 2302
hyporthetical protein mgc27169. [refseq;acc:nm_176782] 1782 206.332 203.874 1.01206
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 852 193.114 185.412 1.04154
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] 674 226.497 214.355 1.05664
i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] 1162 220.758 215.097 1.02632
immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] 1888 218.414 216.131 1.01056
immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] 1706 223.846 220.847 1.01358
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 926 217.942 210.139 1.03713
importin 4. [refseq;acc:nm_024658] 2356 220.921 221.863 1.00426
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 2709 220.521 220.395 1.00057
importin 8; ran-binding protein 8. [refseq;acc:nm_006390] 2710
importin 9. [refseq;acc:nm_018085] 2860 0.00001 0.00001 1
importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] 1952 211.647 213.724 1.00981
importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 2780 0.00001 0.00001 1
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 1018 217.361 210.554 1.03233
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 1016 217.369 210.561
importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] 1970 211.62 213.683 1.00975
importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] 2523 201.96 201.488 1.00234
importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] 1676 218.691 215.645 1.01413
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] 1474 218.582 214.427 1.01938
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 1459 192.336 188.637 1.01961

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/