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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 980 to 1029 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
Interaction Map
red
green
network_comparison
245 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] PDSS1 Subtracted Low confidence 211.794 202.482 9.312
246 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] no value High confidence 243.583 267.528 23.945
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 Divided 237.312 212.363 1.11748
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Low confidence 162.755 155.476 1.04682
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] OSR1 Subtracted 217.69 208.421 9.269
247 60s ribosomal protein l12. [swissprot;acc:p30050] no value High confidence 243.583 267.527 23.944
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Divided Low confidence 162.755 155.476 1.04682
phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (ec 2.7.1.38) (phosphorylase kinase gamma subunit 1). [swissprot;acc:q16816] PHKG1 Subtracted 217.957 227.209 9.252
rna-binding protein. [refseq;acc:nm_019027] no value Divided High confidence 237.302 212.41 1.11719
248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Subtracted 243.583 267.527 23.944
lbp-9. [refseq;acc:nm_014553] TFCP2L1 Low confidence 219.758 210.509 9.249
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Divided 162.755 155.476 1.04682
249 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] DUOX1 210.487 201.076 1.0468
ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP High confidence 237.302 212.41 1.11719
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Subtracted 226.109 202.333 23.776
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] TFCP2 Low confidence 219.749 210.503 9.246
250 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] AMY1C 219.742 210.498 9.244
diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] DGAT1 Divided 210.443 201.051 1.04671
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR High confidence 237.302 212.41 1.11719
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] PLDN Subtracted 210.693 186.95 23.743
251 40s ribosomal protein s20. [swissprot;acc:p17075] RPS20 243.5 267.21 23.71
nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] NOX5 Divided Low confidence 210.415 201.035 1.04666
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 High confidence 186.172 166.661 1.11707
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] UBP1 Subtracted Low confidence 219.722 210.484 9.238
252 cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] CYBB Divided 210.414 201.035 1.04665
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 High confidence 237.292 212.457 1.11689
mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Subtracted 228 204.333 23.667
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] SNRPB2 Low confidence 202.654 193.53 9.124
253 mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Divided High confidence 228 204.333 1.11583
nadph oxidase 4. [refseq;acc:nm_016931] NOX4 Low confidence 210.413 201.035 1.04665
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] NFYB Subtracted High confidence 251.679 228.037 23.642
parafibromin. [refseq;acc:nm_024529] CDC73 Low confidence 214.015 204.916 9.099
254 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 High confidence 227.999 204.357 23.642
nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] NOX3 Divided Low confidence 210.414 201.035 1.04665
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] ATP2C2 Subtracted 218.785 209.763 9.022
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B Divided High confidence 200.691 179.88 1.11569
255 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 Subtracted 227.999 204.366 23.633
nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] NOX1 Divided Low confidence 210.413 201.035 1.04665
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 Subtracted 200.699 191.678 9.021
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A Divided High confidence 200.691 179.88 1.11569
256 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 Subtracted 227.999 204.37 23.629
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 Divided 204.357 1.11569
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A Low confidence 199.376 190.521 1.04648
sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] SOAT2 Subtracted 208.469 199.455 9.014
257 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] DDOST Divided High confidence 200.691 179.88 1.11569
jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] JAG2 Subtracted Low confidence 218.715 209.71 9.005
tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] TPM3 Divided 201.316 192.404 1.04632
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] CMPK Subtracted High confidence 242.14 265.697 23.557
258 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] AK3

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/