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

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/