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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
2 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] Ranked Divided High confidence 1 15 28 1.86667
Squared Subtracted 407289 263351 143938
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Ranked Divided Low confidence 0 8906 21883 2.45711
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 5865 14977 2.55362
Rooted Subtracted Low confidence 29.3087 7.61577 21.6929
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Ranked 9607 20617 11010
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Measured 23818.1 19621.3 4196.8
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Squared Divided High confidence 5.61325 0.00001 561325
Rooted 12.4097 1240970
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Measured 1 450.5 2394.5 5.31521
Squared 48.0356 1357.07 28.2513
Rooted 21.225 48.9336 2.30547
Subtracted 27.7086
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Squared Low confidence 0 414704 386144 28560
3 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Rooted High confidence 36.9188 6.85565 30.0631
anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Low confidence 45.6289 66 20.3711
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Squared High confidence 135280 170628 35348
cab2. [refseq;acc:nm_033419] Ranked 21866 10950 10916
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Divided Low confidence 1 223 330 1.47982
cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Measured 2399.5 543.5 4.4149
Ranked Subtracted 223 330 107
Squared Divided 1362.75 69.9153 19.4914
Rooted 48.9847 23.3131 2.10117
Subtracted 25.6716
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Ranked Divided High confidence 15 28 1.86667
Squared Subtracted 407289 263351 143938
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Measured 41482.5 33356.5 8126
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Divided 2597.5 698.5 3.71868
Squared 1596.92 115.48 13.8285
Rooted 50.9657 26.4292 1.92839
Subtracted 24.5365
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Squared Divided Low confidence 0 0.00001 1.87479 187479
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Measured 89 8900000
Rooted 9.43398 943398
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Measured Subtracted 1 21185 28492 7307
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Ranked Divided 0 9607 20617 2.14604
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 4475.84 11083.9 2.47638
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Measured Subtracted 23818.1 19621.3 4196.8
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Low confidence 5106.93 7500.75 2393.82
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Divided High confidence 0.00001 109 10900000
rad50-interacting protein 1. [refseq;acc:nm_021930] Ranked Subtracted 1 337 232 105
rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565] Squared Low confidence 0 220988 197937 23051
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided High confidence 5.61325 0.00001 561325
Rooted 12.4097 1240970
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Squared Subtracted Low confidence 1 333506 475045 141539
4 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Measured 0 2082 4356 2274
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 1 36474.3 43509.4 7035.1
cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Ranked Divided 223 330 1.47982
cytochrome c oxidase polypeptide viic, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p15954] Squared Subtracted 0 273831 295570 21739

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/