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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Gene green description Hugo Rank red Network Comparison Type Value Type Interaction Map Filtered network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 3228 in total
green  : 0.00001
red  : 0.00001
Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
network_comparison  : 1
description
Hugo
Rank
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] PLCB4 3126
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] ALDH1L1 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] YWHAE 3088
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428] HPGD 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] CYP27B1 3079
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193] HSD3B7 3147
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] no value 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] HSD17B10 3180
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393] PTS 2904
60s ribosomal protein l37a. [swissprot;acc:p12751] no value 2959
69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084] ICA1 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] AKAP5 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] ACVR1 3050
adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979] SH2B2 2870
aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353] ALDH3B1 3222
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] ALDH3B2 2992
aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278] AOX1 2960
alpha crystallin a chain. [swissprot;acc:p02489] CRYAA 2875
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] CRYAB 3082
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] ASPSCR1 2829
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] APPBP2 3191
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] ARIH2 2798
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [swissprot;acc:p18859] ATP5J 2893
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964] ATP5L 2834
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] AUH 2913
ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1] FNDC3A 3117
ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] RNF144B 2968
barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531] BANF1 2804
bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061] TEGT 2950
bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745] BCOR 2776
beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1] UPB1 3145
bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] BMP5 3069
bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004] BMP6 2896
bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] BMP7 3128
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] BMP8A 2773
brca1 associated protein. [refseq;acc:nm_006768] BRAP 3161
bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4] BRPF3 3149
bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696] BRD1 3139
bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7] NUB1 3214
bup protein. [refseq;acc:nm_012071] COMMD3 2911
calmodulin. [swissprot;acc:p02593] no value 2928
camp responsive element binding protein-like 2. [refseq;acc:nm_001310] CREBL2 3078
camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [swissprot;acc:p10644] PRKAR1A 3089
carcinoma related gene. [refseq;acc:nm_016041] DERL2 3179
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786] CPT2 2885
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0] CSNK1G1 2830
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368] CSNK1G2 2986
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4] CSNK1G3 2901
caveolin-1. [swissprot;acc:q03135] CAV1 3099

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/