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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Network Comparison Type Gene Value Type description Rank network_comparison green Filtered Interaction Map red
Results: HTML CSV LaTeX Showing element 1327 to 1376 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
network_comparison
green
red
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 686 1.05602 125.389 132.413
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 685
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 616 1.05999 202.132 214.257
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 680 1.05602 125.389 132.413
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 684
homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 615 1.05999 202.132 214.257
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 679 1.05602 125.389 132.413
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 681
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 682
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 617 1.05997 202.135 214.257
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 683 1.05602 125.389 132.413
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 632 1.05979 202.166 214.254
homeobox protein meis1. [swissprot;acc:o00470] 1783 1.01206 203.874 206.332
homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] 1784
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] 1788
homeobox protein nkx-6.1. [swissprot;acc:p78426] 2859 1 0.00001 0.00001
homeobox protein otx1. [swissprot;acc:p32242] 1520 1.01778 240.098 244.367
homeobox protein otx2. [swissprot;acc:p32243] 1521 1.01776 240.212 244.478
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] 1709 1.01346 195.385 198.014
homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] 1128 1.02733 215.399 221.286
homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] 1129 1.02732 215.401 221.285
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 107 1.24907 201.998 252.309
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 104 1.24926 202.016 252.371
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 108 1.24902 201.995 252.296
homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [swissprot;acc:q15011] 3196 1 0.00001 0.00001
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 1.00969 207.529 209.539
hormone sensitive lipase (ec 3.1.1.-) (hsl). [swissprot;acc:q05469] 3172 1 0.00001 0.00001
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 289 1.10486 246.892 272.781
hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] 2231 1.00633 223.246 221.842
hsgcn1 (fragment). [sptrembl;acc:q99736] 2712 1.00057 220.395 220.521
hskin17 protein. [refseq;acc:nm_012311] 1697 1.01367 214.69 217.624
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 2258 1.00582 225.191 223.888
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] 1486 1.01906 203.989 207.877
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 1.00936 190.73 188.961
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 1993 1.00943 190.835 189.052
huntingtin interacting protein c. [refseq;acc:nm_012272] 195 1.13748 200.417 227.971
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] 729 1.05187 219.708 208.874
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] 949 1.0354 209.826 217.253
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 179 1.16476 194.79 226.884
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 2415 1.00359 218.984 218.2
hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507] 2191 1.00662 208.162 209.54
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 1.024 226.399 221.093
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 1.0283 238.486 231.922
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 1.03774 241.288 232.512
hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775] 1640 1.01464 197.364 194.516

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/