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 [...,...].
    Rank Gene Network Comparison Type Hugo description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 875 to 924 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		red
    		network_comparison
    		green
    110 Divided MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Squared 19321 1.54043 12542.6
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Measured 4366.44 1.35116 5899.76
    Subtracted no value pnas-18. [sptrembl;acc:q9bzu3] Squared 87787.3 29631.5 58155.8
    JPH3 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Rooted 33.9632 15.5377 18.4255
    NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Ranked 209.299 39.888 249.187
    PPP1R8 nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Measured 17385.9 2496.7 14889.2
    111 Divided CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Rooted 49.2923 1.26585 62.3969
    DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Ranked 332.925 1.24563 267.274
    MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Squared 19321 1.54043 12542.6
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Measured 4366.44 1.35116 5899.76
    Subtracted ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Squared 79779.8 28304.2 108084
    CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Measured 12365.2 2459.7 14824.9
    GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Ranked 209.299 39.888 249.187
    JPH2 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Rooted 33.9632 15.5377 18.4255
    112 Divided CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 49.3267 1.26537 62.4167
    MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Squared 19321 1.54043 12542.6
    PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Ranked 332.874 1.24557 267.246
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Measured 4366.44 1.35116 5899.76
    Subtracted ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 11757.8 2405.69 9352.11
    CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Squared 96730.5 27443.8 69286.7
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Ranked 275.754 39.846 235.908
    SMPD2 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] Rooted 33.9632 15.5377 18.4255
    113 Divided no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Measured 4366.44 1.35116 5899.76
    ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Rooted 80.4705 1.26165 101.526
    KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Ranked 332.874 1.24557 267.246
    MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Squared 19321 1.54043 12542.6
    Subtracted ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Measured 4800.81 2331.9 7132.71
    CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Squared 96602.7 27391.5 69211.2
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Ranked 194.372 39.832 234.204
    TMEM33 db83 protein. [swissprot;acc:p57088] Rooted 33.9632 15.5377 18.4255
    114 Divided no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Squared 19321 1.54043 12542.6
    ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Rooted 80.4705 1.26165 101.526
    KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked 332.874 1.24557 267.246
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Measured 4300.47 1.35048 5807.72
    Subtracted no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 13768.2 2302.2 11466
    ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Squared 67438.6 26741.6 40697
    B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Ranked 229.818 37.447 267.265
    GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Rooted 40.225 15.5199 24.7051
    115 Divided KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Ranked 332.874 1.24557 267.246
    MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Measured 21185 1.34491 28492
    MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Squared 19321 1.54043 12542.6
    SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Rooted 80.4705 1.26165 101.526
    Subtracted no value pnas-18. [sptrembl;acc:q9bzu3] Measured 13680.5 2270.9 11409.6
    small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Squared 72886.3 25658.2 98544.5
    DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Rooted 21.4476 15.4983 36.9459
    HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Ranked 277.546 37.085 240.461
    116 Divided AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Rooted 80.4705 1.26165 101.526
    GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Ranked 268.565 1.24545 334.483
    MYH13 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Squared 19321 1.54043 12542.6
    PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Measured 21185 1.34491 28492

    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/