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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 62324 to 62373 of 66312 in total
Interaction Map  : Low confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
network_comparison
green
4563 MRPL46 mitochondrial ribosomal protein l46; chromosome 15 open reading frame 4. [refseq;acc:nm_022163] Subtracted Measured 7613.42 139.47 7752.89
NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Squared 31573.7 830.2 30743.5
NOTCH1 neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Divided Measured 8074.17 1.0176 8216.3
STARD13 star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Ranked 200.368 1.00793 198.792
Subtracted 1.576
4564 BCAT1 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Squared 47359.9 829 46530.9
NOTCH2 neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Divided Measured 8074.17 1.0176 8216.3
RNF20 ring finger protein 20. [refseq;acc:nm_019592] Ranked 187.776 1.0079 186.305
RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Squared 45355.4 1.01921 44500.7
SSBP3 single-stranded dna-binding protein 3 (sequence-specific single- stranded-dna-binding protein). [swissprot;acc:q9bww4] Subtracted Measured 9202.76 139.04 9063.72
STX16 syntaxin 16 (syn16). [swissprot;acc:o14662] Rooted 71.9366 1.5553 73.4919
TACC3 transforming acidic coiled-coil-containing protein 3 (eric-1). [swissprot;acc:q9y6a5] Divided 70.5615 1.02176 72.0966
VPS4B skd1 protein (vacuolar sorting protein 4b). [swissprot;acc:o75351] Subtracted Ranked 204.897 1.573 206.47
4565 ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Squared 40421.6 826.7 39594.9
RPL19 60s ribosomal protein l19. [swissprot;acc:p14118] Ranked 206.719 1.57 208.289
SEC24D protein transport protein sec24d (sec24-related protein d). [swissprot;acc:o94855] Divided 202.352 1.00789 200.767
SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Rooted 75.1763 1.02174 76.811
SMAD1 mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797] Measured 7676.22 1.01757 7811.08
TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Squared 45355.4 1.01921 44500.7
TNC tenascin precursor (tn) (hexabrachion) (cytotactin) (neuronectin) (gmem) (ji) (miotendinous antigen) (glioma-associated-extracellular matrix antigen) (gp 150-225) (tenascin-c) (tn-c). [swissprot;acc:p24821] Subtracted Measured 9202.76 139.04 9063.72
TPP2 tripeptidyl-peptidase ii (ec 3.4.14.10) (tpp-ii) (tripeptidyl aminopeptidase). [swissprot;acc:p29144] Rooted 72.6647 1.5538 74.2185
4566 no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Divided 75.177 1.02174 76.8115
CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Measured 9432.85 1.01756 9270.11
HSPA4 heat shock 70 kda protein 4 (heat shock 70-related protein apg-2) (hsp70ry). [swissprot;acc:p34932] Ranked 202.41 1.00778 200.848
Subtracted 1.562
IMMP2L imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Divided Squared 43890.8 1.01919 43064.6
Subtracted 826.2
SSBP2 single-stranded dna-binding protein 2 (sequence-specific single- stranded-dna-binding protein 2). [swissprot;acc:p81877] Measured 9202.7 139.02 9063.68
TH1L th1-like; th1 drosophila homolog; th1-like (drosophila homolog); negative elongation factor proteins c and d. [refseq;acc:nm_016397] Rooted 73.5878 1.553 75.1408
4567 HSPH1 heat-shock protein 105 kda (heat shock 110 kda protein) (antigen ny-co-25). [swissprot;acc:q92598] Divided Ranked 202.407 1.00776 200.848
Subtracted 1.559
MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Divided Measured 7375.6 1.01755 7505.02
ORMDL2 ormdl2. [refseq;acc:nm_014182] Subtracted Squared 44063.8 825.8 43238
PGM3 phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Divided Rooted 75.6338 1.02172 77.2763
RPL8 60s ribosomal protein l8. [swissprot;acc:p25120] Squared 46171.9 1.01917 45303.4
SSBP4 single-stranded dna-binding protein 4. [swissprot;acc:q9bwg4] Subtracted Measured 9202.69 139.02 9063.67
SUV39H2 histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] Rooted 73.7722 1.5511 75.3233
4568 CTNNB1 beta-catenin (pro2286). [swissprot;acc:p35222] 69.5675 1.5503 71.1178
DLC1 rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Divided Ranked 200.361 1.00774 198.822
GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Subtracted 202.587 1.548 201.039
KLHL20 kelch-like protein x. [swissprot;acc:q9y2m5] Divided Rooted 70.1712 1.02169 71.6931
NUP214 nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658] Measured 7753.16 1.01755 7889.24
PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted 8705.7 139.01 8566.69
SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Divided Squared 45893.9 1.01916 45031
U2AF2 splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368] Subtracted 45716.1 825.8 44890.3
4569 no value ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Ranked 202.587 1.548 201.039
AGPAT2 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Divided Squared 46616.1 1.01914 45740.5
ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Subtracted 40393.7 823.3 39570.4
ASRGL1 asparaginase-like 1 protein. [refseq;acc:nm_025080] Divided Ranked 206.65 1.00772 208.245
CDK8 cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Measured 7581.3 1.01753 7714.23

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
- Hugo is the HGNC identifier if it exists
- 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/