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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Rank Value Type Filtered Gene green description Interaction Map Network Comparison Type network_comparison red
Results: HTML CSV LaTeX Showing element 1 to 50 of 14920 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
Value Type
Filtered
green
description
network_comparison
red
1 Measured 0 0.00001 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 36400000 364
1 2394.5 rad50-interacting protein 1. [refseq;acc:nm_021930] 5.31521 450.5
Ranked 0 15915 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 3.70633 4294
1 24 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 2.4 10
Squared 0 7.16592 cab2. [refseq;acc:nm_033419] 716592 0.00001
1 1357.07 rad50-interacting protein 1. [refseq;acc:nm_021930] 28.2513 48.0356
Rooted 0 0.00001 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 1907880 19.0788
1 48.9336 rad50-interacting protein 1. [refseq;acc:nm_021930] 2.30547 21.225
2 Measured 0 174 cab2. [refseq;acc:nm_033419] 17400000 0.00001
1 2394.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 5.31521 450.5
Ranked 0 14977 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 2.55362 5865
1 28 mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 1.86667 15
Squared 0 0.00001 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 561325 5.61325
1 1357.07 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 28.2513 48.0356
Rooted 0 0.00001 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 1240970 12.4097
1 48.9336 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 2.30547 21.225
3 Measured 0 109 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 10900000 0.00001
1 698.5 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 3.71868 2597.5
Ranked 0 11083.9 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 2.47638 4475.84
1 28 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 1.86667 15
Squared 0 0.00001 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 561325 5.61325
1 115.48 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 13.8285 1596.92
Rooted 0 0.00001 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 1240970 12.4097
1 26.4292 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1.92839 50.9657
4 Measured 0 89 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 8900000 0.00001
1 698.5 hbs1-like. [refseq;acc:nm_006620] 3.71868 2597.5
Ranked 0 21883 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 2.45711 8906
1 28 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1.86667 15
Squared 0 2.81207 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 281207 0.00001
1 115.48 hbs1-like. [refseq;acc:nm_006620] 13.8285 1596.92
Rooted 0 10.4403 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 1044030 0.00001
1 26.4292 hbs1-like. [refseq;acc:nm_006620] 1.92839 50.9657
5 Measured 0 89 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 8900000 0.00001
1 339.5 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 3.39764 1153.5
Ranked 0 11965.7 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 2.17144 5510.5
1 28 cytohesin 4. [swissprot;acc:q9uia0] 1.86667 15
Squared 0 1.87479 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 187479 0.00001
1 27.2805 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 11.544 314.926
Rooted 0 9.43398 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 943398 0.00001
1 18.4255 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1.84327 33.9632
6 Measured 0 89 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 8900000 0.00001
1 339.5 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 3.39764 1153.5
Ranked 0 15339.2 ubiquitin protein ligase. [refseq;acc:nm_130466] 2.03897 7523
1 28 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 1.86667 15
Squared 0 1.87479 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 187479 0.00001
1 27.2805 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 11.544 314.926
Rooted 0 9.43398 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 943398 0.00001
1 18.4255 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1.84327 33.9632
7 Measured 0 43 sedlin. [swissprot;acc:o14582] 4300000 0.00001
1 339.5 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 3.39764 1153.5

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/