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 7836 to 7885 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1959 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
oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] Ranked 211.633 213.703 1.00978
phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] Rooted 65.7394 67.5854 1.02808
rd protein. [swissprot;acc:p18615] Measured 4374.32 4126.96 1.05994
1967 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 3678.56 3470.55
choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] Ranked 211.632 213.702 1.00978
cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] Squared 24782.4 27081.1 1.09276
histidine-rich membrane protein ke4. [swissprot;acc:q92504] Rooted 63.8906 65.6826 1.02805
1968 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Squared 24782.4 27081.1 1.09276
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Measured 4374.32 4126.96 1.05994
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] Rooted 63.8906 65.6826 1.02805
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Ranked 211.633 213.703 1.00978
1969 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Measured 4374.32 4126.96 1.05994
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Squared 24782.4 27081.1 1.09276
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Rooted 63.8903 65.6821 1.02804
1970 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Measured 4374.32 4126.96 1.05994
importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] Ranked 211.62 213.683 1.00975
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Squared 24782.4 27081.1 1.09276
microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] Rooted 63.8904 65.6822 1.02804
1971 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] 59.346 61.0071 1.02799
creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Ranked 198.258 196.346 1.00974
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Squared 24782.4 27081.1 1.09276
j domain containing protein 1. [swissprot;acc:q9ukb3] Measured 4374.32 4126.96 1.05994
1972 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Squared 24782.4 27081.1 1.09276

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/