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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Value Type Interaction Map Gene green Filtered Rank description Network Comparison Type network_comparison red
Results: HTML CSV LaTeX Showing element 582 to 631 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Network Comparison Type  : Divided
green
Rank
description
network_comparison
red
134.527 963 cyclin g1 (cyclin g). [swissprot;acc:p51959] 1.0343 130.066
964 serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]
134.713 980 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 1.03396 130.289
136.846 909 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 1.03823 142.077
136.922 1445 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 1.02003 134.233
140.692 915 trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 1.03798 146.036
144.041 558 ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 1.06628 135.087
144.538 2670 transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 1.00102 144.391
144.552 2678 ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 1.00098 144.411
144.553 2677 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 144.412
144.56 2680 transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 1.00096 144.422
144.564 2682 transforming protein n-ras. [swissprot;acc:p01111] 1.00095 144.427
151.009 2506 44050 protein. [refseq;acc:nm_178832] 1.0025 151.386
2507 nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]
153.371 846 methyltransferase like 2. [refseq;acc:nm_018396] 1.04184 147.211
847 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]
848 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]
849 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]
153.671 28 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 1.31416 201.949
155.961 733 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 1.05154 164
156.153 1319 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 1.02304 159.75
156.275 1322 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 1.02294 159.86
156.421 1324 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] 1.02284 159.993
156.884 1007 ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 1.03296 162.055
158.868 53 transcription factor jun-b. [swissprot;acc:p17275] 1.26611 201.144
158.941 54 transcription factor jun-d. [swissprot;acc:p17535] 1.26425 200.941
160.957 42 proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 1.2714 204.641
43 jun dimerization protein. [refseq;acc:nm_130469]
161.046 44 fos-related antigen 2. [swissprot;acc:p15408] 1.2707
161.051 45 protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 1.27066
161.068 46 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 1.27053 204.642
161.452 818 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] 1.04422 168.592
162.665 2140 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 1.00692 161.547
163.187 2294 protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 1.00527 162.331
163.554 1452 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 1.01978 160.381
163.712 2295 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] 1.00523 162.86
163.8 2203 symplekin. [swissprot;acc:q92797] 1.00651 162.741
164.211 1463 pnas-18. [sptrembl;acc:q9bzu3] 1.01959 161.056
164.46 1117 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 1.02754 168.989
164.467 1118 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 1.02753 168.995
164.507 1123 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 1.0275 169.031
164.917 931 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 1.03637 159.13
164.951 933 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 1.03635 159.165
165.058 2250 likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] 1.00606 164.064
165.623 224 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] 1.12285 185.969
165.898 1159 proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] 1.02641 170.28
166.351 300 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 1.10196 150.959
166.372 301 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 1.10193 150.982
166.393 2635 pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 1.00132 166.612
166.661 251 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 1.11707 186.172

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/