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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1275 to 1324 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    319 MRPL44 mitochondrial ribosomal protein l44. [refseq;acc:nm_022915] Subtracted Low confidence 216.283 8.11 208.173
    RPL19 60s ribosomal protein l19. [swissprot;acc:p14118] Divided High confidence 240.73 1.09969 264.729
    320 CDH1 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 241.892 1.0995 265.96
    MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Subtracted 88.2482 22.0168 110.265
    PHKG2 phosphorylase b kinase gamma catalytic chain, testis/liver isoform (ec 2.7.1.38) (phk-gamma-t) (phosphorylase kinase gamma subunit 2) (psk-c3). [swissprot;acc:p15735] Divided Low confidence 217.756 1.04117 226.722
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Subtracted 202.057 8.105 193.952
    321 no value c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Divided High confidence 241.892 1.09949 265.959
    DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Subtracted Low confidence 209.495 8.021 201.474
    SNORD23 glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] Divided 207.402 1.04108 199.219
    TRO trophinin. [swissprot;acc:q12816] Subtracted High confidence 88.2482 22.0168 110.265
    322 DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Divided 86.7483 1.09948 78.8995
    GGPS1 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Subtracted Low confidence 209.518 7.964 201.554
    NUDT21 cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] Divided 212.262 1.04055 203.991
    RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Subtracted High confidence 231.969 21.905 210.064
    323 no value 60s ribosomal protein l23a. [swissprot;acc:p29316] Divided 241.884 1.09947 265.945
    C20orf43 protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] Subtracted Low confidence 200.482 7.964 208.446
    ITGB1BP2 integrin beta-1 binding protein 2 (melusin) (mstp015). [swissprot;acc:q9ukp3] Divided 212.262 1.04055 203.991
    RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Subtracted High confidence 242.238 21.872 264.11
    324 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
    RAB3GAP2 rab3 gtpase-activating protein, non-catalytic subunit. [refseq;acc:nm_012414] Divided Low confidence 212.262 1.04055 203.991
    RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] High confidence 243.944 1.09941 268.195
    SPSB4 spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] Subtracted Low confidence 219.655 7.892 211.763
    325 AFF2 fragile x mental retardation 2 protein (protein fmr-2) (fmr2p) (ox19 protein) (fragile x e mental retardation syndrome protein). [swissprot;acc:p51816] 219.599 7.876 211.723
    MRPL13 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] High confidence 241.828 21.792 263.62
    MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Divided 243.944 1.09941 268.195
    STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Low confidence 199.905 1.04051 192.123
    326 AFF3 laf-4 protein (lymphoid nuclear protein related to af4). [swissprot;acc:p51826] Subtracted 219.598 7.876 211.722
    DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Divided 199.343 1.04047 191.59
    RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] High confidence 241.899 1.09932 265.924
    RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] Subtracted 241.828 21.792 263.62
    327 AFF4 all1 fused gene from 5q31. [refseq;acc:nm_014423] Low confidence 219.598 7.876 211.722
    POLR2A dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Divided High confidence 243.817 1.09903 267.962
    RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Subtracted 241.83 21.785 263.615
    TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Divided Low confidence 197.221 1.04034 189.574
    328 no value putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Subtracted High confidence 240.801 21.539 262.34
    AFF1 af-4 protein (proto-oncogene af4) (fel protein). [swissprot;acc:p51825] Low confidence 219.597 7.875 211.722
    DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Divided High confidence 258.437 1.09888 235.183
    SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Low confidence 203.162 1.04031 195.289
    329 EXOC7 exocyst complex component exo70. [swissprot;acc:q9upt5] 204.124 1.04025 212.339
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Subtracted High confidence 191.644 21.452 170.192
    NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Divided 312 1.09859 284
    SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Subtracted Low confidence 203.162 7.873 195.289
    330 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] High confidence 224.657 21.422 203.235
    CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Divided 312 1.09859 284
    RGN senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Low confidence 221.437 1.04015 212.889
    SPSB1 spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106] Subtracted 219.556 7.864 211.692
    331 CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] High confidence 224.647 21.405 203.242
    CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Divided 312 1.09859 284
    GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Low confidence 200.249 1.04007 192.535
    NME7 nucleoside diphosphate kinase 7 (ec 2.7.4.6) (ndk 7) (ndp kinase 7) (nm23-h7). [swissprot;acc:q9y5b8] Subtracted 210.796 7.861 202.935

    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/