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 Value Type Rank Network Comparison Type description red Interaction Map Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
red
green
network_comparison
1590 Subtracted prefoldin subunit 1. [swissprot;acc:o60925] 5875.75 6302.76 427.01
1591 Divided multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] 6364.01 6819.38 1.07155
Subtracted secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] 5875.75 6302.76 427.01
1592 Divided 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] 5853.1 6271.79 1.07153
Subtracted choline dehydrogenase. [refseq;acc:nm_018397] 5875.75 6302.76 427.01
1593 Divided proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] 4977.77 5333.78 1.07152
Subtracted colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] 6520.83 6946.75 425.92
1594 Divided transportin-sr; importin 12. [refseq;acc:nm_012470] 5184.94 5555.76 1.07152
Subtracted glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] 5933.25 6358.78 425.53
1595 Divided proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] 6351.32 6805.39 1.07149
Subtracted dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 3760.3 4185.82 425.52
1596 Divided enigma protein; lim domain protein. [refseq;acc:nm_005451] 5665.34 6070.32 1.07148
Subtracted cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 5659.22 6084.68 425.46
1597 Divided eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] 5665.34 6070.32 1.07148
Subtracted 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 6038.46 6463.9 425.44
1598 Divided lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] 5068.17 5430.41 1.07147
Subtracted mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212] 5923.66 6349.04 425.38
1599 Divided 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] 5184.45 5554.97 1.07147
Subtracted 26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524] 5923.66 6349.04 425.38
1600 Divided 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] 6336.22 6788.96 1.07145
Subtracted wd-repeat protein bing4. [swissprot;acc:o15213] 4066.56 4491.65 425.09
1601 Divided spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] 5232.14 5605.8 1.07142
Subtracted cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 5660.17 6085.22 425.05
1602 Divided spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] 5232.14 5605.8 1.07142
Subtracted 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] 5819.39 6244.37 424.98
1603 Divided 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
Subtracted porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] 4913.07 5337.95 424.88
1604 Divided malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] 6176.82 6617.91 1.07141
Subtracted phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] 6260.43 6685.05 424.62
1605 Divided 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
Subtracted phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 6259.8 6684.31 424.51
1606 Divided 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 5232.99 5606.53 1.07138
Subtracted phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] 6259.8 6684.3 424.5
1607 Divided 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
Subtracted sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 4379.28 4803.59 424.31
1608 Divided ubiquitin. [swissprot;acc:p02248] 6158.22 6597.55 1.07134
Subtracted transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 7019.78 7444.06 424.28
1609 Divided 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 5826.74 6242.44 1.07134
Subtracted serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] 6297.05 6721.08 424.03
1610 Divided eif-5a2 protein. [refseq;acc:nm_020390] 6222.4 6665.83 1.07126
Subtracted proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] 6079.19 6503.12 423.93
1611 Divided cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 5497.73 5132.35 1.07119
Subtracted molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] 6079.19 6503.12 423.93
1612 Divided eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] 6212.98 6655.12 1.07116
Subtracted anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] 6079.19 6503.12 423.93
1613 Divided mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 6035.6 6464.5 1.07106
Subtracted 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 6079.19 6503.12 423.93
1614 Divided nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] 6035.6 6464.5 1.07106
Subtracted proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] 6079.19 6503.12 423.93
1615 Divided lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] 6035.6 6464.5 1.07106

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/