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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Network Comparison Type Gene Rank description Interaction Map Value Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 25824 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1602 spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] Measured 5232.14 5605.8 1.07142
1603 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Squared 17081.4 18947.6 1.10925
fibulin-1 precursor. [swissprot;acc:p23142] Rooted 75.958 78.6278 1.03515
heat shock factor binding protein 1. [swissprot;acc:o75506] Ranked 216.62 213.22 1.01595
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Measured 5232.14 5605.8 1.07142
1604 lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] Squared 29262.5 32458.3 1.10921
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] Measured 6176.82 6617.91 1.07141
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] Rooted 64.0052 66.254 1.03513
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Ranked 214.984 211.614 1.01593
1605 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 217.322 213.916 1.01592
itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Measured 6176.82 6617.91 1.07141
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Squared 30908.9 34282.7 1.10915
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Rooted 64.0052 66.254 1.03513
1606 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] Measured 5232.99 5606.53 1.07138
apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Ranked 207.916 204.662 1.0159
dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690] Rooted 64.0052 66.254 1.03513
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Squared 30908.9 34282.7 1.10915
1607 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]
phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] Rooted 64.0052 66.254 1.03513
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Ranked 214.982 211.622 1.01588
putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] Measured 5232.99 5606.53 1.07138
1608 heat shock cognate 71 kda protein. [swissprot;acc:p11142] Squared 30908.9 34282.7 1.10915
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Rooted 99.0527 95.6982 1.03505
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Ranked 208.106 204.867 1.01581
ubiquitin. [swissprot;acc:p02248] Measured 6158.22 6597.55 1.07134
1609 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 5826.74 6242.44
proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] Rooted 65.5919 67.884 1.03494
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Ranked 208.113 204.876 1.0158
wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] Squared 28992.5 32145.6 1.10876
1610 eif-5a2 protein. [refseq;acc:nm_020390] Measured 6222.4 6665.83 1.07126
hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Squared 15639.2 17338.5 1.10866
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Rooted 67.4766 69.831 1.03489
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Ranked 208.122 204.886 1.01579
1611 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Measured 5497.73 5132.35 1.07119
heat shock factor binding protein 1. [swissprot;acc:o75506] Squared 27263.5 30225.7 1.10865
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Rooted 67.4958 69.8487 1.03486
p10-binding protein. [refseq;acc:nm_024491] Ranked 221.313 217.877 1.01577
1612 brain protein 16. [refseq;acc:nm_016458] Squared 26202.2 29043.8 1.10845
enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Ranked 221.426 224.902 1.0157
eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] Measured 6212.98 6655.12 1.07116
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Rooted 67.5045 69.8568 1.03485
1613 hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] Ranked 182.378 185.241 1.0157
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Measured 6035.6 6464.5 1.07106
neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Squared 15399.5 17067.9 1.10834
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Rooted 67.511 69.8628 1.03484
1614 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Ranked 217.233 213.897 1.0156
nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] Measured 6035.6 6464.5 1.07106
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Squared 15399.5 17067.9 1.10834
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Rooted 54.1932 56.0802 1.03482
1615 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Ranked 246.38 242.596 1.0156

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/