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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Value Type green Filtered description Interaction Map red network_comparison Gene Rank Network Comparison Type
Results: HTML CSV LaTeX Showing element 1 to 50 of 77072 in total
Value Type  : Measured
green  : 0
Network Comparison Type  : Subtracted
Filtered
description
Interaction Map
red
network_comparison
Rank
0 brca1 associated protein. [refseq;acc:nm_006768] High confidence 0 0 502
carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615] Low confidence 37 37 648
carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] 649
cobw-like protein. [refseq;acc:nm_018491] 0 0 839
dok-like protein. [refseq;acc:nm_024872] High confidence 35 35 386
ero1-like. [refseq;acc:nm_014584] 82 82 316
gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920] Low confidence 0 0 838
gamma-glutamyltransferase. [sptrembl;acc:q14390] 841
gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440] 842
gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268] 837
gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269] 843
h2a histone family, member j isoform 1. [refseq;acc:nm_018267] High confidence 501
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001] 495
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261] 494
histone h2a; h2a histone family, member r. [refseq;acc:nm_170745] 497
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 499
Low confidence 13 13 777
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 364 364 88
Low confidence 170
mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] High confidence 0 0 496
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Low confidence 286 286 200
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] 201
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] High confidence 154 154 206
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 18 18 429
rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] 0 0 500
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 60 60 338
tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] Low confidence 2.31962 2.31962 822
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] High confidence 154 154 207
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] 0 0 498
Low confidence 840
1 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [swissprot;acc:q15147] High confidence 3126
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] 2922
14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [swissprot;acc:p42655] 3088
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428] 2855
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] 3079
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193] 3147
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 2756
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] 2802
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714] 3180
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393] 2904
60s ribosomal protein l37a. [swissprot;acc:p12751] 2959
69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084] 3227
a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588] 2788
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771] 3050
adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979] 2870
aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353] 3222
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 2992
aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278] 2960
alpha crystallin a chain. [swissprot;acc:p02489] 2875
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] 3082

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/