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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1630 to 1679 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
102 rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Rooted Divided 1 47.6504 36.9304 1.29028
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Squared 0 61.6678 132.922 2.15545
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Rooted 12.0669 15.6768 1.29916
103 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Measured 1 2353.63 3225.65 1.3705
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted Subtracted 19.9625 35.798 15.8355
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Ranked Divided 0 7495.26 9130.38 1.21815
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] Subtracted 18809.5 16764.2 2045.3
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Measured 630.942 327.517 303.425
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] Squared Divided 1 407289 263351 1.54656
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Subtracted 0 79185.5 77891.7 1293.8
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Rooted Divided 17.1172 22.2036 1.29715
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 1 60.8365 77.7233 1.27758
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Measured Subtracted 11068 8508.5 2559.5
symplekin. [swissprot;acc:q92797] Squared 124118 88668.8 35449.2
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Rooted 0 27.4578 22.8323 4.6255
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Squared Divided 61.6678 132.922 2.15545
transcription factor jun-b. [swissprot;acc:p17275] Ranked Subtracted 1 201.144 158.868 42.276
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Measured Divided 0 197.333 290.667 1.47298
trophinin. [swissprot;acc:q12816] Ranked 1 88.2482 110.265 1.24949
104 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] Squared Subtracted 0 8620.27 7355.46 1264.81
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Measured 1 11068 8508.5 2559.5
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Squared Divided 407289 263351 1.54656
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Rooted 0 13.7413 17.8164 1.29656
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Ranked 1 252.371 202.016 1.24926
jun dimerization protein. [refseq;acc:nm_130469] Rooted 60.8365 77.7233 1.27758
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Squared Subtracted 121579 87259.3 34319.7
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Divided 0 0.70501 1.50296 2.13183
musashi 2 isoform a. [refseq;acc:nm_138962] Measured 1 4241.57 5810.79 1.36996
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 0 5106.93 7500.75 1.46874
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Ranked 9545 7868 1.21314
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Rooted Subtracted 1 19.9625 35.798 15.8355
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] Ranked 0 18809.5 16764.2 2045.3
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Measured 688.436 385.626 302.81
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Ranked 1 256.228 298.438 42.21
tigger transposable element derived 6. [refseq;acc:nm_030953] Rooted 0 13.0605 17.6725 4.612
105 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] Ranked Divided 17410.5 14360 1.21243
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Measured Subtracted 5427.25 5130.58 296.67
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Squared Divided 1 407289 263351 1.54656
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 0 2.36686 4.90793 2.0736
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Subtracted 600.627 1860.93 1260.3
fos-related antigen 2. [swissprot;acc:p15408] Measured Divided 3233.86 2208.1 1.46454
Rooted 1 60.8675 77.7168 1.27682
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 0 25.8353 33.3747 1.29183
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Ranked 1 266.716 333.165 1.24914
musashi 1. [refseq;acc:nm_002442] Measured 4241.57 5810.79 1.36996
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Subtracted 11068 8508.5 2559.5
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Squared 90432.9 56304.2 34128.7
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Rooted 63.7477 48.1588 15.5889
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Ranked 0 11853.5 9808.86 2044.64
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Rooted 13.0525 17.6565 4.604

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/