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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7812 to 7861 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1953 uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Measured 5888.32 6245.89 1.06073
1954 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Squared 12789.3 13977.2 1.09288
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Rooted 61.3382 63.0786 1.02837
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Measured 5888.32 6245.89 1.06073
voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] Ranked 211.632 213.703 1.00979
1955 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] Measured 5195.3 5510.67 1.0607
histone deacetylase 4 (hd4). [swissprot;acc:p56524] Rooted 61.3383 63.0785 1.02837
proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] Squared 28220.9 30841.9 1.09287
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Ranked 211.633 213.703 1.00978
1956 histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Rooted 61.3383 63.0785 1.02837
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062] Measured 4689.78 4973.44 1.06048
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Squared 27944.1 30539.3 1.09287
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Ranked 211.633 213.703 1.00978
1957 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Rooted 69.6016 71.5707 1.02829
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Squared 12050.4 13169.1 1.09284
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Ranked 211.633 213.703 1.00978
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] Measured 7019.78 7444.06 1.06044
1958 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] Ranked 211.633 213.703 1.00978
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Squared 12175.3 13305.6 1.09284
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Rooted 69.5996 71.5683 1.02829
splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] Measured 5448.35 5777.35 1.06039
1959 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] Ranked 211.633 213.703 1.00978
fad synthetase. [refseq;acc:nm_025207] Squared 12175.3 13305.6 1.09284
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Rooted 69.6016 71.5707 1.02829
splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081] Measured 5448.35 5777.35 1.06039
1960 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Squared 12175.3 13305.6 1.09284
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] Rooted 69.5947 71.5619 1.02827
golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] Ranked 211.633 213.703 1.00978
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Measured 5448.35 5777.35 1.06039
1961 14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] Rooted 61.3419 63.0743 1.02824
alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] Ranked 211.633 213.703 1.00978
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Squared 12175.3 13305.6 1.09284
splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368] Measured 5448.35 5777.35 1.06039
1962 atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] Rooted 63.5623 65.3574 1.02824
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Squared 12175.3 13305.6 1.09284
c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] Measured 5941.24 6297.78 1.06001
methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] Ranked 211.632 213.702 1.00978
1963 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 211.633 213.703
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Squared 12175.3 13305.6 1.09284
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Measured 4374.32 4126.96 1.05994
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] Rooted 65.7244 67.5801 1.02823
1964 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] 62.1627 63.9151 1.02819
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Squared 12175.3 13305.6 1.09284
pp3111 protein. [refseq;acc:nm_022156] Measured 4374.32 4126.96 1.05994
rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] Ranked 211.633 213.703 1.00978
1965 40s ribosomal protein s23. [swissprot;acc:p39028] Squared 12300.5 13441.9 1.09279
alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] Ranked 224.432 222.258 1.00978
doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] Rooted 63.9035 65.7029 1.02816
syntaxin 18. [swissprot;acc:q9p2w9] Measured 4374.32 4126.96 1.05994
1966 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Squared 12300.5 13441.9 1.09279

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/