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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 647 to 696 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Value Type
    		description
    		red
    		green
    		network_comparison
    162 Squared homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 173408 242989 1.40126
    Rooted heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 52.7642 61.9019 1.17318
    163 Measured melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 23693.7 18263 1.29736
    Ranked eap30 subunit of ell complex. [refseq;acc:nm_007241] 209.299 249.187 1.19058
    Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 173408 242989 1.40126
    Rooted eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 52.7702 61.8915 1.17285
    164 Measured melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 23693.7 18263 1.29736
    Ranked liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 209.299 249.187 1.19058
    Squared homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 173408 242989 1.40126
    Rooted mad protein (max dimerizer). [swissprot;acc:q05195] 55.646 65.1534 1.17086
    165 Measured melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 23693.7 18263 1.29736
    Ranked glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 209.299 249.187 1.19058
    Squared homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 173408 242989 1.40126
    Rooted max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 55.6486 65.1478 1.1707
    166 Measured melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 23693.7 18263 1.29736
    Ranked gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 209.299 249.187 1.19058
    Squared homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 173408 242989 1.40126
    Rooted max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 55.6495 65.1458 1.17064
    167 Measured melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 23693.7 18263 1.29736
    Ranked glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 209.299 249.187 1.19058
    Squared homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 173408 242989 1.40126
    Rooted max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 55.65 65.1448 1.17062
    168 Measured melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 23693.7 18263 1.29736
    Ranked gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 82.5916 98.0548 1.18722
    Squared retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 173408 242989 1.40126
    Rooted small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 56.3709 65.8949 1.16895
    169 Measured melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 23693.7 18263 1.29736
    Ranked apg3p; pc3-96 protein. [refseq;acc:nm_022488] 82.5916 98.0548 1.18722
    Squared symplekin. [swissprot;acc:q92797] 124118 88668.8 1.39979
    Rooted cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 62.762 53.7761 1.1671
    170 Measured melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 23693.7 18263 1.29736
    Ranked nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 227.199 192.715 1.17894
    Squared cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 96730.5 69286.7 1.39609
    Rooted b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 53.4993 45.9227 1.16499
    171 Measured 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] 23693.7 18263 1.29736
    Ranked nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 227.202 192.823 1.17829
    Squared ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 96602.7 69211.2 1.39577
    Rooted lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 61.6639 71.7355 1.16333
    172 Measured trophinin. [swissprot;acc:q12816] 23693.7 18263 1.29736
    Ranked cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 174.667 205.556 1.17685
    Squared likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] 121579 87259.3 1.39331
    Rooted splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 56.7592 65.9889 1.16261
    173 Measured breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 4579.34 5940.64 1.29727
    Ranked small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 227.032 193.056 1.17599
    Squared septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] 82624.3 115061 1.39258
    Rooted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 145.551 168.796 1.1597
    174 Measured mad protein (max dimerizer). [swissprot;acc:q05195] 4455.95 5774.03 1.2958
    Ranked dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 335 286 1.17133
    Squared sedlin. [swissprot;acc:o14582] 112820 157033 1.39189
    Rooted pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 145.551 168.796 1.1597

    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/