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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2962 to 3011 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
741 gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Measured 5768.32 6434.78 1.11554
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Ranked 223.58 235.027 1.0512
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Squared 23894.7 27894.5 1.16739
742 brain protein 44. [swissprot;acc:o95563] Ranked 126.215 120.078 1.05111
eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Measured 4131.04 4607.9 1.11543
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Squared 31406.6 36662.8 1.16736
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Rooted 67.0234 71.5506 1.06755
743 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Squared 31406.6 36662.8 1.16736
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Measured 4131.04 4607.9 1.11543
katanin p60 subunit a 1. [refseq;acc:nm_007044] Rooted 54.4988 51.0573 1.0674
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Ranked 126.215 120.078 1.05111
744 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Squared 31406.6 36662.8 1.16736
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Measured 12515.4 11221.1 1.11535
dynactin 4. [refseq;acc:nm_032486] Rooted 55.2242 51.7372 1.0674
septin 6. [swissprot;acc:q14141] Ranked 126.604 120.463 1.05098
745 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Squared 31406.6 36662.8 1.16736
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Measured 4086.6 4557.68 1.11527
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Ranked 214.679 225.568 1.05072
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

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/