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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 [...,...].
    Gene description Rank Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1808 to 1857 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 785 NET1 244.447 233.508 1.04685
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 333 NEUROD1 312 284 1.09859
    neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 329 NEUROD2
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 334 NEUROD4
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 332 NEUROD6
    neuromedin u receptor 2. [refseq;acc:nm_020167] 2991 NMUR2 0.00001 0.00001 1
    neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 444 NAV1 223.801 207.549 1.0783
    neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] 443 NAV2 223.79 207.539
    neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 445 NAV3 223.801 207.549
    neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] 1183 HPCA 225.103 230.928 1.02588
    neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 1272 CHRNA2 171.231 167.177 1.02425
    neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 1276 CHRNA3
    neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 1275 CHRNA4
    neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] 1268 CHRNA6
    neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 465 CHRNA7 248.152 267.226 1.07686
    neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] 1367 FREQ 223.887 228.799 1.02194
    neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840] 2484 KIF5A 218.093 218.72 1.00287
    neuronal shc. [refseq;acc:nm_016848] 2127 SHC3 221.248 222.788 1.00696
    neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] 2336 TMOD2 229.258 230.294 1.00452
    neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 481 NETO1 237.109 254.667 1.07405
    neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 480 NETO2
    neurotrimin precursor (hnt). [swissprot;acc:q9p121] 1498 no value 224.022 219.924 1.01863
    neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] 1649 PRSS12 219.062 215.942 1.01445
    neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] 1419 SLC3A1 203.979 208.229 1.02084
    nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963] 2616 NFKBIA 202.821 202.54 1.00139
    nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653] 2653 NFKBIB 201.452 201.674 1.0011
    nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221] 2651 NFKBIE 201.37 201.594 1.00111
    ngd5 protein homolog (cgi-53). [swissprot;acc:q9y366] 3133 IFT52 0.00001 0.00001 1
    nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] 1622 NHP2L1 228.611 225.185 1.01521
    nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] 2301 NMNAT3 217.392 218.498 1.00509
    nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] 2257 QPRT 212.563 211.315 1.00591
    nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 2649 no value 213.63 213.874 1.00114
    nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062] 2499 NOB1 231.414 230.76 1.00283
    nipsnap1 protein. [swissprot;acc:q9bpw8] 2770 NIPSNAP1 0.00001 0.00001 1
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] 2918 GBAS
    nitrilase 1. [refseq;acc:nm_005600] 2579 NIT1 213.422 213.75 1.00154
    nitrogen fixation cluster-like. [refseq;acc:nm_014301] 1269 ISCU 171.231 167.177 1.02425
    nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [refseq;acc:nm_177400] 2909 NKX6-2 0.00001 0.00001 1
    nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] 526 RRP1 250.538 234.401 1.06884
    nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] 800 SCP2 221.965 212.404 1.04501
    nostrin. [refseq;acc:nm_052946] 162 NOSTRIN 209.299 249.187 1.19058
    nov protein homolog precursor (novh) (nephroblastoma overexpressed gene protein homolog). [swissprot;acc:p48745] 2970 NOV 0.00001 0.00001 1
    ns1-associated protein 1. [refseq;acc:nm_006372] 249 SYNCRIP 237.302 212.41 1.11719
    nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] 3184 SP100 0.00001 0.00001 1
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 147 no value 50.7983 42.3003 1.2009
    nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] 2743 NFE2L3 198.278 198.321 1.00022
    nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494] 2742 NFE2L1
    nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653] 2654 NFKB2 201.452 201.674 1.0011
    nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] 2652 NFKB1 201.451 201.673
    nuclear factor related to kappa b binding protein. [refseq;acc:nm_006165] 2823 NFRKB 0.00001 0.00001 1

    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/