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 network_comparison red green
Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
Filtered
network_comparison
red
green
1 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Divided High confidence 0 3.70633 4294 15915
carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Low confidence 1 2 16 32
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Subtracted High confidence 107 215 322
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 223 330
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 0 12977 8906 21883
Low confidence
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Divided 2.55362 5865 14977
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 1 2.4 10 24
2 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Subtracted 0 11621 4294 15915
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 1 107 223 330
hbs1-like. [refseq;acc:nm_006620] High confidence 215 322
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Divided Low confidence 1.47982 223 330
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] High confidence 1.86667 15 28
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Low confidence 0 2.45711 8906 21883
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 2.55362 5865 14977
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Subtracted Low confidence 11010 9607 20617
3 cab2. [refseq;acc:nm_033419] High confidence 10916 21866 10950
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Divided Low confidence 1 1.47982 223 330
cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Subtracted 107
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Divided High confidence 1.86667 15 28
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Low confidence 0 2.14604 9607 20617
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Subtracted 11010
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Divided High confidence 2.47638 4475.84 11083.9
rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted 1 105 337 232
4 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Divided Low confidence 1.47982 223 330
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 1.86667 15 28
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Subtracted Low confidence 107 223 330
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided High confidence 0 2.45711 8906 21883
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted Low confidence 9112 5865 14977
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Divided 2.14604 9607 20617
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Subtracted High confidence 10363 11525 21888
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 105 337 232
5 cytohesin 4. [swissprot;acc:q9uia0] Divided 1.86667 15 28
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted Low confidence 0 9070 22286 13216
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Divided 1 1.47982 223 330
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Subtracted 78 318 240
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] High confidence 0 10363 11525 21888
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Divided 2.17144 5510.5 11965.7
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 1.82499 10889.4 19873
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Subtracted High confidence 1 97 212 309
6 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Divided 1.86667 15 28
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted Low confidence 0 9070 22286 13216
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 9112 5865 14977
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 1 78 318 240
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Divided 1.325
protein x 0004. [refseq;acc:nm_016301] Subtracted High confidence 97 212 309
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Divided Low confidence 0 1.71877 5575.71 9583.37
ubiquitin protein ligase. [refseq;acc:nm_130466] High confidence 2.03897 7523 15339.2
7 cab2. [refseq;acc:nm_033419] 1.99689 21866 10950
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Low confidence 1.69451 11543 6812

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/