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