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.


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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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 930 to 979 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
Interaction Map
red
green
network_comparison
233 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] CSRP3 Divided High confidence 239.32 267.842 1.11918
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] NFYC Low confidence 209.649 200.129 1.04757
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 Subtracted 201.41 191.974 9.436
234 40s ribosomal protein s23. [swissprot;acc:p39028] RPS23 High confidence 243.944 268.195 24.251
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] CHRAC1 Divided 287.41 256.835 1.11905
cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850] CYP51A1 Low confidence 208.851 199.38 1.0475
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] DUOX2 Subtracted 210.504 201.086 9.418
235 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] MRPS12 High confidence 243.944 268.195 24.251
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] PAH Divided 227.357 254.15 1.11785
u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] SNRPA Subtracted Low confidence 202.727 193.31 9.417
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] SNRPB2 Divided 202.654 193.53 1.04715
236 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] DUOX1 Subtracted 210.487 201.076 9.411
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] RBBP7 High confidence 252.644 228.42 24.224
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] CASK Divided Low confidence 212.056 202.524 1.04707
pp3111 protein. [refseq;acc:nm_022156] DUS1L High confidence 227.357 254.15 1.11785
237 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] DGAT1 Subtracted Low confidence 210.443 201.051 9.392
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] MRPL3 High confidence 242.011 266.18 24.169
single-minded homolog 1. [swissprot;acc:p81133] SIM1 Divided Low confidence 212.056 202.524 1.04707
syntaxin 18. [swissprot;acc:q9p2w9] STX18 High confidence 227.357 254.15 1.11785
238 metastasis-associated protein mta1. [swissprot;acc:q13330] MTA1 Subtracted 252.512 228.356 24.156
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 Divided Low confidence 200.699 191.678 1.04706
rd protein. [swissprot;acc:p18615] no value High confidence 227.357 254.15 1.11785
tensin. [refseq;acc:nm_022648] TNS1 Subtracted Low confidence 215.258 205.872 9.386
239 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] POLR2A High confidence 243.817 267.962 24.145
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] DUOX2 Divided Low confidence 210.504 201.086 1.04684
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] GSTO1 High confidence 227.357 254.15 1.11785
nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] NOX5 Subtracted Low confidence 210.415 201.035 9.38
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] AIG1 Divided High confidence 227.357 254.15 1.11785
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] RBBP4 Subtracted 252.39 228.297 24.093
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 Low confidence 210.414 201.035 9.379
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value Divided 162.755 155.476 1.04682
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] ATP5F1 High confidence 227.357 254.15 1.11785
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] CDH1 Subtracted 241.892 265.96 24.068
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 Divided Low confidence 162.755 155.476 1.04682
nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] NOX3 Subtracted 210.414 201.035 9.379
242 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] no value High confidence 241.892 265.959 24.067
calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] WDR92 Low confidence 214.887 205.509 9.378
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 Divided 162.755 155.476 1.04682
j domain containing protein 1. [swissprot;acc:q9ukb3] DNAJC12 High confidence 227.357 254.15 1.11785
243 60s ribosomal protein l23a. [swissprot;acc:p29316] no value Subtracted 241.884 265.945 24.061
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided Low confidence 162.755 155.476 1.04682
nadph oxidase 4. [refseq;acc:nm_016931] NOX4 Subtracted 210.413 201.035 9.378
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] SNX13 Divided High confidence 227.357 254.15 1.11785
244 60s ribosomal protein l5. [swissprot;acc:p46777] RPL5 Subtracted 241.899 265.924 24.025
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2 Divided 227.357 254.15 1.11785
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 Low confidence 162.755 155.476 1.04682
nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] NOX1 Subtracted 210.413 201.035 9.378
245 60s ribosomal protein l19. [swissprot;acc:p14118] RPL19 High confidence 240.73 264.729 23.999
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 Divided Low confidence 162.755 155.476 1.04682
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 High confidence 226.109 202.333 1.11751

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/