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

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/