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 [...,...].
green description Gene Rank red Hugo Network Comparison Type network_comparison Value Type Interaction Map Filtered
Results: HTML CSV LaTeX Showing element 1 to 50 of 3228 in total
green  : 0.00001
red  : 0.00001
Network Comparison Type  : Divided
network_comparison  : 1
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
description
Rank
Hugo
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] 3126 PLCB4
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] 2922 ALDH1L1
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 YWHAE
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428] 2855 HPGD
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 CYP27B1
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193] 3147 HSD3B7
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 2756 no value
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 HSD17B10
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393] 2904 PTS
60s ribosomal protein l37a. [swissprot;acc:p12751] 2959 no value
69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084] 3227 ICA1
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 AKAP5
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 ACVR1
adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979] 2870 SH2B2
aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353] 3222 ALDH3B1
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 2992 ALDH3B2
aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278] 2960 AOX1
alpha crystallin a chain. [swissprot;acc:p02489] 2875 CRYAA
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] 3082 CRYAB
alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [refseq;acc:nm_024083] 2829 ASPSCR1
amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [refseq;acc:nm_006380] 3191 APPBP2
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 2798 ARIH2
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [swissprot;acc:p18859] 2893 ATP5J
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964] 2834 ATP5L
au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698] 2913 AUH
ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1] 3117 FNDC3A
ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] 2968 RNF144B
barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531] 2804 BANF1
bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061] 2950 TEGT
bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745] 2776 BCOR
beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1] 3145 UPB1
bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] 3069 BMP5
bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004] 2896 BMP6
bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] 3128 BMP7
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 2773 BMP8A
brca1 associated protein. [refseq;acc:nm_006768] 3161 BRAP
bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4] 3149 BRPF3
bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696] 3139 BRD1
bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7] 3214 NUB1
bup protein. [refseq;acc:nm_012071] 2911 COMMD3
calmodulin. [swissprot;acc:p02593] 2928 no value
camp responsive element binding protein-like 2. [refseq;acc:nm_001310] 3078 CREBL2
camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [swissprot;acc:p10644] 3089 PRKAR1A
carcinoma related gene. [refseq;acc:nm_016041] 3179 DERL2
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786] 2885 CPT2
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0] 2830 CSNK1G1
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368] 2986 CSNK1G2
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4] 2901 CSNK1G3
caveolin-1. [swissprot;acc:q03135] 3099 CAV1

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
- Hugo is the HGNC identifier if it exists
- 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/