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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 151 to 200 of 502 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 0
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    151 no value u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 7502.08 6461.83 1.16098
    152 similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 11438 13277.1 1.16079
    153 TUBG1 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] 7879.3 6789.92 1.16044
    154 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 10883 12622.8 1.15986
    155 REEP6 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 12759.4 11028.8 1.15692
    156 TUB tubby protein homolog. [swissprot;acc:p50607] 12303.7 10641.7 1.15618
    157 no value transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 18079 15652 1.15506
    158 NME2P1 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 10060.2 11616.4 1.15469
    159 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 5813.32 6706.32 1.15361
    160 no value ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 11732 13530.6 1.15331
    161 ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 5781.93 6660.63 1.15197
    162 no value putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 12301.4 10680.5 1.15176
    163 TFCP2 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] 8409.21 9668.79 1.14979
    164 no value dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] 11971.7 10412.4 1.14975
    165 ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 13255.4 15183.2 1.14544
    166 BOLA2B my016 protein. [sptrembl;acc:q9h3k6] 5561.19 6366.91 1.14488
    167 SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 12157.6 13890.3 1.14252
    168 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] 7091.75 6217.28 1.14065
    169 GPT alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 9875.43 11256.8 1.13988
    170 FCER2 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 11364 12941 1.13877
    171 no value lamin b2. [swissprot;acc:q03252] 12135.4 13802 1.13733
    172 SNAI2 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] 12225.7 13893.1 1.13638
    173 no value suppressor of actin 1. [refseq;acc:nm_014016] 19088.1 16804.6 1.13589
    174 ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] 13248.5 11666.4 1.13561
    175 thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]
    176 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 13068 11528 1.13359
    177 KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 14922.7 13174.5 1.1327
    178 no value integral membrane protein cii-3b. [sptrembl;acc:o75609] 14951.6 13204.2 1.13234
    179 MVK mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] 9473.01 10723.7 1.13203
    180 NOVA1 rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] 8407.67 9516.92 1.13193
    181 no value importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 14864.7 16820.7 1.13159
    182 NADK putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 11573.8 10231.3 1.13121
    183 no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 11613 13133.5 1.13093
    184 similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 6279.56 5569.42 1.12751
    185 zinc finger protein 277. [swissprot;acc:q9nrm2]
    186 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 11935.1 10592.8 1.12672
    187 ADSSL1 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 9955.22 11213.7 1.12641
    188 RPL15 60s ribosomal protein l15. [swissprot;acc:p39030] 11745.2 13203.1 1.12413
    189 SALL4 sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] 10634.4 9465 1.12355
    190 no value high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] 18809.5 16764.2 1.122
    191 sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
    192 CCT6A t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] 12715.9 11333.2
    193 GTF3A transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] 10899.5 12217.4 1.12091
    194 no value kappa b-ras 1. [refseq;acc:nm_020345] 12657.7 11299.1 1.12024
    195 MRPS22 mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 13942.8 15586.4 1.11788
    196 no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 11064.2 9897.84 1.11784
    197 importin 4. [refseq;acc:nm_024658] 12337.6 13788.9 1.11763
    198 RPL10L ribosomal protein l10-like protein. [refseq;acc:nm_080746] 11781.5 10545.3 1.11723
    199 no value 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 11781.8 10545.7 1.11721
    200 MTRF1 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 8786.74 7870.3 1.11644

    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/