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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
1602 TOP3A Rooted dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 61.8653 64.0396 1.03515
1603 no value Ranked heat shock factor binding protein 1. [swissprot;acc:o75506] 216.62 213.22 1.01595
CSNK2A2 Squared casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 17081.4 18947.6 1.10925
FBLN1 Rooted fibulin-1 precursor. [swissprot;acc:p23142] 75.958 78.6278 1.03515
PGM3 Measured phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] 5232.14 5605.8 1.07142
1604 CLK2 Ranked protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] 214.984 211.614 1.01593
LIN7A Squared lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] 29262.5 32458.3 1.10921
MLYCD Measured malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] 6176.82 6617.91 1.07141
PIK3C2G Rooted 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 66.254 1.03513
1605 FOXA1 Ranked hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 217.322 213.916 1.01592
ITCH Measured 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 6617.91 1.07141
PIK3C2B Rooted 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 66.254 1.03513
PXMP2 Squared peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] 30908.9 34282.7 1.10915
1606 APOA1BP Ranked apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 207.916 204.662 1.0159
DNM1L Rooted dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690] 64.0052 66.254 1.03513
HSPA2 Squared heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] 30908.9 34282.7 1.10915
MTAP Measured 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 5232.99 5606.53 1.07138
1607 no value Squared heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 30908.9 34282.7 1.10915
CLK3 Ranked protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] 214.982 211.622 1.01588
FTSJ1 Measured putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] 5232.99 5606.53 1.07138
PIK3C2A Rooted phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] 64.0052 66.254 1.03513
1608 CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] 99.0527 95.6982 1.03505
HSPA8 Squared heat shock cognate 71 kda protein. [swissprot;acc:p11142] 30908.9 34282.7 1.10915
TMEM189 Ranked ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 208.106 204.867 1.01581
UBC Measured ubiquitin. [swissprot;acc:p02248] 6158.22 6597.55 1.07134
1609 PSMB5 Rooted 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 67.884 1.03494
PSMD10 Measured 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 5826.74 6242.44 1.07134
UGP2 Ranked utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 208.113 204.876 1.0158
WTAP Squared wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] 28992.5 32145.6 1.10876
1610 EIF5A2 Measured eif-5a2 protein. [refseq;acc:nm_020390] 6222.4 6665.83 1.07126
KRR1 Squared hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 15639.2 17338.5 1.10866
SLC5A5 Rooted sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] 67.4766 69.831 1.03489
UBE2V2 Ranked 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] 208.122 204.886 1.01579
1611 no value Squared heat shock factor binding protein 1. [swissprot;acc:o75506] 27263.5 30225.7 1.10865
CEP70 Ranked p10-binding protein. [refseq;acc:nm_024491] 221.313 217.877 1.01577
PRODH2 Rooted kidney and liver proline oxidase 1. [refseq;acc:nm_021232] 67.4958 69.8487 1.03486
TRIP10 Measured cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 5497.73 5132.35 1.07119
1612 no value Ranked enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] 221.426 224.902 1.0157
Squared brain protein 16. [refseq;acc:nm_016458] 26202.2 29043.8 1.10845
EIF5AP1 Measured eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] 6212.98 6655.12 1.07116
SLC5A8 Rooted solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] 67.5045 69.8568 1.03485
1613 HTATIP2 Ranked 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] 182.378 185.241 1.0157
MRPS22 Measured mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 6035.6 6464.5 1.07106
NETO2 Squared neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 15399.5 17067.9 1.10834
SLC5A6 Rooted sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] 67.511 69.8628 1.03484
1614 no value Measured nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] 6035.6 6464.5 1.07106
FOXA2 Ranked hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] 217.233 213.897 1.0156
NETO1 Squared neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 15399.5 17067.9 1.10834
PDSS1 Rooted trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 54.1932 56.0802 1.03482
1615 HNRNPU Squared heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 15399.5 17067.9 1.10834

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
- Hugo is the HGNC identifier if it exists
- 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/