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 Hugo Gene description Value Type Network Comparison Type Filtered Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 404 to 453 of 502 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 0
    Interaction Map  : High confidence
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    404 no value udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] 9783.63 10111.2 1.03348
    405 UGT2B4 udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]
    406 ENPEP glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]
    407 UGT2B10 udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537]
    408 no value udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]
    409 DIP2B similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] 10598.5 10945.3 1.03272
    410 no value histone h4. [swissprot;acc:p02304] 9611.37 9308.99 1.03248
    411 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 12115.7 12508.3 1.0324
    412 ALAS1 5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] 8546.06 8279.69 1.03217
    413 PTRH2 protein cgi-147. [swissprot;acc:q9y3e5] 5135.25 5298.12 1.03172
    414 no value germ cell-less. [refseq;acc:nm_022471] 10978.8 10644.4 1.03142
    415 transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] 13571.2 13166.3 1.03075
    416 transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] 13607.6 13202 1.03072
    417 LSAMP limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 10854.8 10537.9 1.03007
    418 no value blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 16680.7 17180.3 1.02995
    419 RHD blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 16684 17183 1.02991
    420 no value blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]
    421 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 11186 10866.3 1.02942
    422 GLUL glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 12581.7 12224.2 1.02925
    423 CYLD cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] 5905 6073 1.02845
    424 DPP6 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] 9562.48 9298.93 1.02834
    425 SCRIB scribble. [refseq;acc:nm_015356] 12370.5 12719 1.02817
    426 no value atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] 9412.67 9676.67 1.02805
    427 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 11276.1 11582.7 1.02719
    428 CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 11982.7 12301.2 1.02658
    429 no value 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 12318.7 12631.5 1.02539
    430 splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 11621.7 11913.4 1.0251
    431 histone deacetylase 2 (hd2). [swissprot;acc:q92769] 10043.7 9799.17 1.02495
    432 FBN3 fibrillin 3. [refseq;acc:nm_032447] 930 953 1.02473
    433 no value trinucleotide repeat containing 15. [refseq;acc:nm_015575] 772 754 1.02387
    434 elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] 10028.5 10261.5 1.02323
    435 HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 8770.94 8574.04 1.02296
    436 no value histone h2b.d (h2b/d). [swissprot;acc:q99877] 8770.82 8574.19 1.02293
    437 histone h2b.s (h2b/s). [swissprot;acc:p57053] 8770.41 8574.66 1.02283
    438 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 7759.36 7586.42 1.0228
    439 histone h2b. [refseq;acc:nm_175055] 8770.3 8574.79
    440 histone h2b.e (h2b/e). [swissprot;acc:q99879] 8770.28 8574.81
    441 HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] 8770.14 8574.98 1.02276
    442 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 14570.4 14247.3 1.02268
    443 protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 9141.6 8940.14 1.02253
    444 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 14556.7 14237.8 1.0224
    445 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 7965.06 7790.78 1.02237
    446 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
    447 CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] 12532.2 12808.8 1.02207
    448 C19orf56 protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] 2939 2876 1.02191
    449 ARPC1B arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] 9897.12 9690.83 1.02129
    450 no value small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 11290.8 11525.8 1.02081
    451 CHL1 cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] 14010.2 13737.2 1.01987
    452 no value neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]
    453 TAF9 transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]

    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/