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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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