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 762 to 811 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		red
    		green
    		network_comparison
    381 TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Divided 200.586 183.423 1.09357
    382 DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Subtracted 253.852 234.808 19.044
    TAF7L tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Divided 200.791 183.66 1.09328
    383 RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 237.862 217.739 1.09242
    TRUB1 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Subtracted 236.245 255.113 18.868
    384 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 227.575 208.756 18.819
    E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Divided 266.421 244.236 1.09083
    385 E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
    SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Subtracted 227.575 208.756 18.819
    386 RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Divided 242.238 264.11 1.09029
    RPS9 40s ribosomal protein s9. [swissprot;acc:p46781] Subtracted 238.986 257.784 18.798
    387 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Divided 242.238 264.11 1.09029
    ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 56.6768 75.3531 18.6763
    388 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Divided 227.575 208.756 1.09015
    MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Subtracted 56.7244 75.3948 18.6704
    389 MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 56.7252 75.3954 18.6702
    SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Divided 227.575 208.756 1.09015
    390 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 56.7841 75.447 18.6629
    MRPL13 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Divided 241.828 263.62 1.09011
    391 RPS16 40s ribosomal protein s16. [swissprot;acc:p17008]
    TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Subtracted 225.719 207.072 18.647
    392 POLR3C polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 239.092 257.705 18.613
    RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Divided 241.83 263.615 1.09008
    393 POLR3F dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Subtracted 238.921 257.327 18.406
    TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Divided 225.719 207.072 1.09005
    394 CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Subtracted 207.889 226.226 18.337
    DPP9 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Divided 218.827 238.407 1.08948
    395 DPP8 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
    PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] Subtracted 207.908 226.218 18.31
    396 no value putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Divided 240.801 262.34 1.08945
    RPA1 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Subtracted 207.908 226.218 18.31
    397 CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Divided 110.689 101.613 1.08932
    RPA2 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Subtracted 207.908 226.218 18.31
    398 ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Divided 218.818 238.358 1.0893
    PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Subtracted 207.908 226.218 18.31
    399 CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Divided 207.889 226.226 1.08821
    RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351] Subtracted 207.908 226.218 18.31
    400 CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 207.931 226.209 18.278
    PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] Divided 207.908 226.218 1.08807
    401 MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Subtracted 254.434 236.224 18.21
    RPA1 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Divided 207.908 226.218 1.08807
    402 NDC80 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Subtracted 231.802 249.983 18.181
    RPA2 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Divided 207.908 226.218 1.08807
    403 MACF1 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Subtracted 228.468 246.338 17.87
    PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Divided 207.908 226.218 1.08807
    404 DST bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Subtracted 228.463 246.33 17.867
    RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351] Divided 207.908 226.218 1.08807
    405 CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 207.931 226.209 1.0879
    GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Subtracted 65.4586 83.0461 17.5875
    406 no value transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Divided 265.634 244.304 1.08731

    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/