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.


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