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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 925 to 974 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
Interaction Map
red
green
network_comparison
232 Divided CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] High confidence 239.336 267.879 1.11926
NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Low confidence 214.032 204.284 1.04772
Subtracted BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] High confidence 226.401 202.094 24.307
CYP51A1 cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850] Low confidence 208.851 199.38 9.471
233 Divided CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] High confidence 239.32 267.842 1.11918
NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Low confidence 209.649 200.129 1.04757
Subtracted no value 60s ribosomal protein l7. [swissprot;acc:p18124] High confidence 235.727 259.984 24.257
SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Low confidence 201.41 191.974 9.436
234 Divided CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] High confidence 287.41 256.835 1.11905
CYP51A1 cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850] Low confidence 208.851 199.38 1.0475
Subtracted DUOX2 dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] 210.504 201.086 9.418
RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] High confidence 243.944 268.195 24.251
235 Divided PAH phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 227.357 254.15 1.11785
SNRPB2 u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Low confidence 202.654 193.53 1.04715
Subtracted MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] High confidence 243.944 268.195 24.251
SNRPA u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] Low confidence 202.727 193.31 9.417
236 Divided CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 212.056 202.524 1.04707
DUS1L pp3111 protein. [refseq;acc:nm_022156] High confidence 227.357 254.15 1.11785
Subtracted DUOX1 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Low confidence 210.487 201.076 9.411
RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] High confidence 252.644 228.42 24.224
237 Divided SIM1 single-minded homolog 1. [swissprot;acc:p81133] Low confidence 212.056 202.524 1.04707
STX18 syntaxin 18. [swissprot;acc:q9p2w9] High confidence 227.357 254.15 1.11785
Subtracted DGAT1 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Low confidence 210.443 201.051 9.392
MRPL3 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] High confidence 242.011 266.18 24.169
238 Divided no value rd protein. [swissprot;acc:p18615] 227.357 254.15 1.11785
NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Low confidence 200.699 191.678 1.04706
Subtracted MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] High confidence 252.512 228.356 24.156
TNS1 tensin. [refseq;acc:nm_022648] Low confidence 215.258 205.872 9.386
239 Divided DUOX2 dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] 210.504 201.086 1.04684
GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] High confidence 227.357 254.15 1.11785
Subtracted NOX5 nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Low confidence 210.415 201.035 9.38
POLR2A dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] High confidence 243.817 267.962 24.145
240 Divided no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 162.755 155.476 1.04682
AIG1 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] High confidence 227.357 254.15 1.11785
Subtracted CYBB 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] Low confidence 210.414 201.035 9.379
RBBP4 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] High confidence 252.39 228.297 24.093
241 Divided ATP5F1 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 227.357 254.15 1.11785
HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Low confidence 162.755 155.476 1.04682
Subtracted CDH1 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] High confidence 241.892 265.96 24.068
NOX3 nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] Low confidence 210.414 201.035 9.379
242 Divided DNAJC12 j domain containing protein 1. [swissprot;acc:q9ukb3] High confidence 227.357 254.15 1.11785
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Low confidence 162.755 155.476 1.04682
Subtracted no value c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] High confidence 241.892 265.959 24.067
WDR92 calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] Low confidence 214.887 205.509 9.378
243 Divided no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 162.755 155.476 1.04682
SNX13 sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] High confidence 227.357 254.15 1.11785
Subtracted no value 60s ribosomal protein l23a. [swissprot;acc:p29316] 241.884 265.945 24.061
NOX4 nadph oxidase 4. [refseq;acc:nm_016931] Low confidence 210.413 201.035 9.378
244 Divided GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] High confidence 227.357 254.15 1.11785
HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 162.755 155.476 1.04682

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/