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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2980 to 3029 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
745 Rooted transcription factor btf3 homolog 3. [swissprot;acc:q13892] 67.0475 71.5566 1.06725
746 Measured rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] 4086.6 4557.68 1.11527
Ranked eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 250.465 238.38 1.0507
Squared hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] 31406.6 36662.8 1.16736
Rooted katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] 54.5195 51.084 1.06725
747 Measured down-regulated in metastasis. [refseq;acc:nm_014503] 4086.6 4557.68 1.11527
Ranked trinucleotide repeat containing 15. [refseq;acc:nm_015575] 250.465 238.38 1.0507
Squared transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] 31401.8 36655.7 1.16731
Rooted sr rich protein. [refseq;acc:nm_032870] 61.4809 65.6088 1.06714
748 Measured ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 12503.3 11212 1.11517
Ranked fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 245.246 233.483 1.05038
Squared breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 23148.8 27021.5 1.1673
Rooted mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] 60.4376 64.4898 1.06705
749 Measured ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] 4565.34 5085.92 1.11403
Ranked exocyst complex component sec15b. [swissprot;acc:q9y2d4] 221.968 211.326 1.05036
Squared cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] 23148.8 27021.5 1.1673
Rooted 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 66.9737 71.4637 1.06704
750 Measured myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] 4565.34 5085.92 1.11403
Ranked exocyst complex component sec15a. [swissprot;acc:q8tag9] 222.138 211.503 1.05028
Squared n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] 21678.4 25303.3 1.16721
Rooted mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] 60.4385 64.49 1.06704
751 Measured myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] 4565.34 5085.92 1.11403
Ranked u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 223.463 212.875 1.04974
Squared ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 20305.9 23689.4 1.16663
Rooted 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 66.9738 71.4638 1.06704
752 Measured nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380] 4565.34 5085.92 1.11403
Ranked step ii splicing factor slu7. [refseq;acc:nm_006425] 223.463 212.875 1.04974
Squared u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 20305.9 23689.4 1.16663
Rooted 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 66.9736 71.4636 1.06704
753 Measured myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] 4565.34 5085.92 1.11403
Ranked lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 224.434 235.583 1.04968
Squared biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 24183.6 28211.1 1.16654
Rooted 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 66.9737 71.4637 1.06704
754 Measured myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] 4565.34 5085.92 1.11403
Ranked microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] 224.434 235.583 1.04968
Squared branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 23958.6 27945.1 1.16639
Rooted 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 66.9737 71.4637 1.06704
755 Measured nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] 4079.81 4545.01 1.11402
Ranked uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] 224.434 235.583 1.04968
Squared branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 23966.4 27952.2 1.16631
Rooted 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 66.9737 71.4637 1.06704
756 Measured topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] 4725.28 5261.06 1.11339
Ranked cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] 224.434 235.583 1.04968
Squared transducin-like enhancer protein 4. [swissprot;acc:q04727] 31298 36502 1.16627
Rooted 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 66.9737 71.4637 1.06704
757 Measured signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] 5622.89 6260.02 1.11331
Ranked bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] 224.434 235.583 1.04968
Squared splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 20248.9 23608.3 1.16591
Rooted ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 60.4457 64.4918 1.06694
758 Measured dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 3760.3 4185.82 1.11316

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/