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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 38536 in total
Network Comparison Type  : Divided
Rank
Value Type
description
Interaction Map
Filtered
red
green
network_comparison
4 Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence 0 0.00001 89 8900000
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 1 2399.5 543.5 4.4149
Ranked cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 223 330 1.47982
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 15 28 1.86667
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 8906 21883 2.45711
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Low confidence 9607 20617 2.14604
Squared guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 0.00001 0.823905 82390.5
hbs1-like. [refseq;acc:nm_006620] High confidence 1 1596.92 115.48 13.8285
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 1362.75 69.9153 19.4914
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 0 0.00001 2.81207 281207
Rooted hbs1-like. [refseq;acc:nm_006620] 1 50.9657 26.4292 1.92839
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 0 0.00001 9.43398 943398
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 1 48.9847 23.3131 2.10117
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 0 0.00001 10.4403 1044030
5 Measured homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 89 8900000
jumonji protein. [swissprot;acc:q92833] Low confidence 17.5166 1751660
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence 1 1153.5 339.5 3.39764
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 736.5 2113.5 2.86965
Ranked cytohesin 4. [swissprot;acc:q9uia0] High confidence 15 28 1.86667
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 223 330 1.47982
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] High confidence 0 5510.5 11965.7 2.17144
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 10889.4 19873 1.82499
Squared carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615] 0.324024 0.00001 32402.4
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence 0.00001 1.87479 187479
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 314.926 27.2805 11.544
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 128.386 1057.25 8.23493
Rooted guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 0 0.00001 7.68115 768115
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence 9.43398 943398
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 33.9632 18.4255 1.84327
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 27.1385 45.9728 1.69401
6 Measured homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 0 0.00001 89 8900000
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] Low confidence 13 0.00001 1300000
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence 1 1153.5 339.5 3.39764
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 736.5 2113.5 2.86965
Ranked cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] High confidence 15 28 1.86667
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 318 240 1.325
trinucleotide repeat containing 15. [refseq;acc:nm_015575] 0 5575.71 9583.37 1.71877
ubiquitin protein ligase. [refseq;acc:nm_130466] High confidence 7523 15339.2 2.03897
Squared carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] Low confidence 0.324024 0.00001 32402.4
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 0.00001 1.87479 187479
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 314.926 27.2805 11.544
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 128.386 1057.25 8.23493
Rooted carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615] 0 6.08276 0.00001 608276
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 0.00001 9.43398 943398
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 33.9632 18.4255 1.84327
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 27.1385 45.9728 1.69401
7 Measured oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 736.5 2113.5 2.86965
sedlin. [swissprot;acc:o14582] High confidence 0 0.00001 43 4300000
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] 1 1153.5 339.5 3.39764
tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] Low confidence 0 2.31962 0.00001 231962

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/