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 description Gene Network Comparison Type Hugo Value Type red Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1358 to 1407 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    340 myelin gene expression factor 2. [refseq;acc:nm_016132] MYEF2 Ranked 235.383 258.476 1.09811
    nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] PRPF19 Rooted 58.4926 64.8047 1.10791
    ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] RRM2B Squared 32117 40054 1.24713
    341 60s ribosomal protein l9. [swissprot;acc:p32969] no value Ranked 240.243 263.798 1.09805
    homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 Measured 20446.1 24136.4 1.18049
    lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] SSB Rooted 51.9812 57.5858 1.10782
    ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] RRM1 Squared 32056.4 39965.8 1.24673
    342 40s ribosomal protein s20. [swissprot;acc:p17075] RPS20 Ranked 243.5 267.21 1.09737
    hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] HGS Squared 70830.5 56822 1.24653
    homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 Measured 20446.1 24136.4 1.18049
    probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] EBNA1BP2 Rooted 49.2715 54.5757 1.10765
    343 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] no value 50.3169 45.4333 1.10749
    conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] COG7 Squared 70830.5 56822 1.24653
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Measured 20446.1 24136.4 1.18049
    protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] PRMT3 Ranked 241.625 265.136 1.0973
    344 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] no value
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Measured 20446.1 24136.4 1.18049
    isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] IDH2 Squared 37226.9 46400.1 1.24641
    suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] PPAN-P2RY11 Rooted 49.4233 54.7327 1.10743
    345 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] DHX15 56.2615 62.2958 1.10725
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Measured 20446.1 24136.4 1.18049
    sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] SH3GL1 Squared 35793 44595.3 1.24592
    ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] CMPK Ranked 242.14 265.697 1.09729
    346 40s ribosomal protein s3. [swissprot;acc:p23396] RPS3 241.612 265.119
    grb2-related adaptor protein. [swissprot;acc:q13588] GRAP Rooted 61.4282 68.0107 1.10716
    importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] CSE1L Squared 34018.3 42373 1.24559
    septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] SEPT1 Measured 14229.2 16780.7 1.17931
    347 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] TIPRL Rooted 66.4284 60.0004 1.10713
    enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] PRSS7 Measured 4991.02 5885.09 1.17914
    gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] AK3 Ranked 242.14 265.697 1.09729
    small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] SNRPD2 Squared 16573.6 20637.8 1.24522
    348 ad24 protein. [refseq;acc:nm_022451] NOC3L Rooted 49.2558 54.5235 1.10695
    adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] no value Ranked 242.14 265.696 1.09728
    golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] GORASP2 Squared 42566.2 52985.3 1.24477
    splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] SF3B2 Measured 4991.02 5885.09 1.17914
    349 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] DHX15 4714.85 5554.38 1.17806
    sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] SH3GL2 Squared 35533.9 44227 1.24464
    surfeit locus protein 5. [swissprot;acc:q15528] MED22 Ranked 242.14 265.696 1.09728
    u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] LSM4 Rooted 56.0061 61.9704 1.10649
    350 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] ARMET Squared 35508.7 44191.4 1.24452
    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] NAV2 Rooted 61.3383 67.8668 1.10643
    sedlin. [swissprot;acc:o14582] ZNF547 Measured 17396.9 20483.9 1.17745
    zinc finger protein 291. [swissprot;acc:q9by12] SCAPER Ranked 242.14 265.696 1.09728
    351 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] ANKS1B Rooted 61.3352 67.8618 1.10641
    histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] HDC Squared 35508.6 44191.3 1.24452
    peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] PEX1 Ranked 242.14 265.696 1.09728
    synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] no value Measured 17396.9 20483.9 1.17745
    352 40s ribosomal protein s28. [swissprot;acc:p25112] Squared 30682.9 38183.6 1.24446
    bet3 homolog. [swissprot;acc:o43617] TRAPPC3 Measured 17396.9 20483.9 1.17745
    neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] NAV1 Rooted 61.3354 67.8621 1.10641

    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/