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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7014 to 7063 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1754 gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] Rooted 61.8148 63.7722 1.03167
neuronal shc. [refseq;acc:nm_016848] Squared 25629.5 28203.8 1.10044
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Ranked 220.091 217.362 1.01256
1755 adp-ribosylation factor 1. [swissprot;acc:p32889] Squared 25629.5 28203.8 1.10044
chromodomain y-like protein 2. [refseq;acc:nm_152342] Measured 7101.7 7577.75 1.06703
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Ranked 180.609 178.393 1.01242
inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] Rooted 61.8148 63.7722 1.03167
1756 40s ribosomal protein s29. [swissprot;acc:p30054] Measured 3582.57 3357.6 1.067
copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] Rooted 63.1514 65.151 1.03166
heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651] Squared 25629.5 28203.8 1.10044
megf6 (fragment). [sptrembl;acc:o75095] Ranked 221.811 219.09 1.01242
1757 adp-ribosylation factor 3. [swissprot;acc:p16587] Squared 25629.5 28203.8 1.10044
copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] Rooted 63.1552 65.1534 1.03164
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Ranked 180.537 178.325 1.0124
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Measured 7101.15 7576.84 1.06699
1758 chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Ranked 233.45 230.595 1.01238
leng5 protein. [refseq;acc:nm_024075] Rooted 60.1532 62.0558 1.03163
protein sck (fragment). [swissprot;acc:p98077] Squared 25629.5 28203.8 1.10044
1759 heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626]
ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] Ranked 219.37 222.086 1.01238
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Measured 7101.16 7576.87 1.06699
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Rooted 60.1532 62.0558 1.03163
1760 myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] Ranked 233.45 230.595 1.01238
ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830] Squared 25629.5 28203.8 1.10044
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Rooted 60.1532 62.0558 1.03163
thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] Measured 5693.88 6075.25 1.06698
1761 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Squared 25629.5 28203.8 1.10044
electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Measured 7794.41 8316.04 1.06692
myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] Ranked 233.45 230.595 1.01238
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Rooted 60.1532 62.0558 1.03163
1762 nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380] Ranked 233.45 230.595 1.01238
solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [swissprot;acc:q9ugh3] Squared 25629.5 28203.8 1.10044
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Rooted 60.1532 62.0558 1.03163
tumor susceptibility gene 101 protein. [swissprot;acc:q99816] Measured 6122.76 6531.3 1.06672
1763 dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [swissprot;acc:o14733] Squared 25629.5 28203.8 1.10044
dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] Measured 5829.73 6218.45 1.06668
myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] Ranked 233.45 230.595 1.01238
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Rooted 67.2158 69.3348 1.03153
1764 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952]
beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] Measured 5829.61 6218.27 1.06667
mitotic checkpoint protein bub3. [swissprot;acc:o43684] Squared 24216.1 26647.5 1.1004
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Ranked 233.45 230.595 1.01238
1765 beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] Measured 5829.61 6218.27 1.06667
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Ranked 215.698 218.369 1.01238
zinc finger protein 207. [swissprot;acc:o43670] Squared 24216.1 26647.5 1.1004
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Rooted 67.2158 69.3348 1.03153
1766 c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] Ranked 228.932 231.732 1.01223
dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Squared 13979 15381.6 1.10034
hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507] Rooted 67.2158 69.3348 1.03153

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/