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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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