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 [...,...].
    Gene Value Type Rank Interaction Map Filtered description network_comparison Network Comparison Type green red
    Results: HTML CSV LaTeX Showing element 401 to 450 of 14920 in total
    Value Type  : Measured
    Interaction Map  : High confidence
    Network Comparison Type  : Divided
    Rank
    		Filtered
    		description
    		network_comparison
    		green
    		red
    201 0 swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] 1.1958 5690.63 6804.88
    1 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 1.26294 6075.04 4810.22
    202 0 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 1.19421 723.75 606.049
    1 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 1.26269 6076.09 4812.01
    203 0 microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] 1.19408 363 304
    1 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 1.25723 9352.11 11757.8
    204 0 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 1.19395 6685.11 7981.68
    1 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 1.25339 5655.52 4512.19
    205 0 spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] 1.19245 4543.75 5418.2
    1 small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 1.25339 5655.52 4512.19
    206 0 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 1.19157 943.423 1124.15
    1 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 1.24965 4577.5 5720.25
    207 0 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 1.19069 339.154 403.827
    1 splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 1.24946 5961.43 4771.21
    208 0 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 1.19061 5540.2 6596.23
    1 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 1.24907 5082.18 4068.78
    209 0 small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] 1.18717 111 93.5
    1 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 1.24907 5082.18 4068.78
    210 0 transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] 1.18697 887.413 1053.33
    1 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 1.24906 5082.21 4068.82
    211 0 ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 1.18661 2076.5 2464
    1 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 1.24905 5082.27 4068.91
    212 0 ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] 1.18661 2076.5 2464
    1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 1.24896 5553.79 4446.72
    213 0 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] 1.18471 1376.88 1162.21
    1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 1.24896 5553.79 4446.72
    214 0 similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 1.18447 15605.1 13174.7
    1 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 1.24827 5086.49 4074.83
    215 0 zinc finger protein 277. [swissprot;acc:q9nrm2] 1.18447 15605.1 13174.7
    1 transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 1.24717 12888.4 16074
    216 0 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 1.18256 14756 12478
    1 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 1.24714 12886.8 16071.6
    217 0 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1.17199 771.309 903.967
    1 ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 1.24714 12886.8 16071.6
    218 0 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] 1.16907 3118.3 3645.5
    1 transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 1.24712 12886 16070.4
    219 0 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 1.16896 7572.88 8852.4
    1 transforming protein n-ras. [swissprot;acc:p01111] 1.24711 12885.6 16069.8
    220 0 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 1.16178 21730 18704
    1 mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 1.24361 33356.5 41482.5
    221 0 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 1.15998 1643 1905.84
    1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 1.24361 33356.5 41482.5
    222 0 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 1.15728 1735.23 1499.4
    1 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1.24361 33356.5 41482.5
    223 0 hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 1.15407 650.724 750.981
    1 cytohesin 4. [swissprot;acc:q9uia0] 1.24361 33356.5 41482.5
    224 0 60s ribosomal protein l7. [swissprot;acc:p18124] 1.15183 2206.07 1915.27
    1 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 1.24361 33356.5 41482.5
    225 0 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 1.15181 7608 8763
    1 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 1.24114 7279.6 9035

    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
    - 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/