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 7812 to 7861 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
977 prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Ranked Divided 228.953 221.421 1.03402
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Squared Subtracted 19129.8 22652.9 3523.1
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Rooted Divided 61.8392 65.3085 1.0561
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Measured 4115.9 4513.14 1.09651
very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975] Squared 27402.5 31532.3 1.15071
978 disrupter of silencing 10. [refseq;acc:nm_020368] 27403.4 31533.3
fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Subtracted 26127.9 29648.4 3520.5
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Measured 5385.04 5933.65 548.61
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Rooted 64.0132 67.4724 3.4592
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Ranked Divided 228.953 221.421 1.03402
tubby protein homolog. [swissprot;acc:p50607] Subtracted 211.987 204.964 7.023
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Rooted Divided 61.9036 65.3694 1.05599
vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] Measured 6654.42 7296.51 1.09649
979 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Rooted 67.7212 71.51 1.05595
gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Ranked 202.027 195.386 1.03399
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Rooted Subtracted 56.7827 60.2401 3.4574
multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Squared 26127.9 29648.4 3520.5
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Ranked 211.987 204.964 7.023
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Measured 3890.53 4439.07 548.54
very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] Squared Divided 27403.4 31533.4 1.15071
vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] Measured 6654.42 7296.51 1.09649
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] Ranked 130.289 134.713 1.03396
cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Rooted Subtracted 56.7817 60.2369 3.4552
dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Divided 61.9121 65.373 1.0559
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Squared Subtracted 15034.5 18552.2 3517.7
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Ranked 211.987 204.964 7.023
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Measured 5887.52 6434.32 546.8
solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] Squared Divided 27403.6 31533.6 1.15071
vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] Measured 6654.42 7296.51 1.09649
981 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Rooted 61.9129 65.3733 1.05589
cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] Measured 6654.42 7296.51 1.09649
exocyst complex component sec6. [swissprot;acc:o60645] Ranked 207.186 200.398 1.03387
loh1cr12. [refseq;acc:nm_058169] Measured Subtracted 5195.48 5741.63 546.15
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Rooted 56.7817 60.2368 3.4551
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] Squared Divided 27403.1 31533 1.15071
tbc1 domain family member 5. [swissprot;acc:q92609] Ranked Subtracted 211.987 204.964 7.023
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Squared 22626.3 26143 3516.7
982 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Measured Divided 6654.42 7296.51 1.09649
atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] Rooted Subtracted 56.7818 60.2369 3.4551
bystin. [swissprot;acc:q13895] Divided 53.1515 56.1209 1.05587
cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Ranked 243.312 235.351 1.03383
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Squared 30999.6 35666.3 1.15054
rna-binding protein. [refseq;acc:nm_019027] Subtracted 15043.7 18560.1 3516.4
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Ranked 211.987 204.964 7.023
unr protein. [swissprot;acc:o75534] Measured 5195.48 5741.63 546.15
983 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Squared 15043.7 18560.1 3516.4
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Rooted Divided 56.1832 53.2244 1.05559
pbk1 protein. [sptrembl;acc:o76021] Ranked 243.312 235.353 1.03382
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Rooted Subtracted 56.7818 60.2369 3.4551
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Squared Divided 31010.8 35677.6 1.15049

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/