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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5808 to 5857 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
363 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Rooted Subtracted 1 56.48 63.119 6.639
364 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Ranked 0 16684 17183 499
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 1 233.539 253.197 19.658
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Rooted Divided 50.0785 55.3215 1.1047
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Subtracted 0 21.4045 20.3439 1.0606
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Ranked Divided 1 243.208 266.617 1.09625
dok-like protein. [refseq;acc:nm_024872] Measured Subtracted 6102.59 7081.46 978.87
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Squared 0 94.1723 66.6659 27.5064
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Measured Divided 48 51 1.0625
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] Ranked 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Measured 1 5189 6088.47 1.17334
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Rooted Subtracted 60.594 67.2244 6.6304
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Squared Divided 17957.2 22234.1 1.23817
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Subtracted 34068.1 40330.8 6262.7
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Rooted Divided 0 53.8642 56.248 1.04426
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] Measured Subtracted 204.382 154.804 49.578
365 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] Rooted 32.0326 30.9731 1.0595
60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Ranked Divided 1 242.744 266.07 1.09609
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Subtracted 0 16684 17183 499
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Squared Divided 1 17965.8 22243 1.23807
calcyphosine. [swissprot;acc:q13938] Measured 5189 6088.47 1.17334
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Rooted 0 30.3712 31.6971 1.04366
di-ras2. [refseq;acc:nm_017594] Squared Subtracted 1 34068 40330.7 6262.7
docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Measured 6102.59 7081.46 978.87
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Squared 0 93.5732 66.2405 27.3327
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Ranked 1 233.539 253.197 19.658
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Measured Divided 0 48 51 1.0625
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Rooted 1 49.7541 54.9425 1.10428
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Subtracted 63.0715 56.4506 6.6209
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Measured 0 1229.57 1278.36 48.79
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Ranked Divided 7769.96 8139.71 1.04759
tubby protein homolog. [swissprot;acc:p50607] Squared 9661.54 10902.9 1.12848
366 40s ribosomal protein s15a. [swissprot;acc:p39027] Rooted 1 50.5463 45.7763 1.1042
40s ribosomal protein s5. [swissprot;acc:p46782] Ranked 242.473 265.756 1.09602
apical-like protein (apxl protein). [swissprot;acc:q13796] Rooted Subtracted 60.6697 67.2802 6.6105
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Squared Divided 62783.5 50784.1 1.23628
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Ranked Subtracted 233.539 253.197 19.658
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured Divided 5189 6088.47 1.17334
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Squared Subtracted 0 48.5538 75.7214 27.1676
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Measured 1 6102.59 7081.46 978.87
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Ranked Divided 0 8614.89 9017.27 1.04671
guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] Subtracted 7386.71 6895.44 491.27
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] Measured Divided 48 51 1.0625
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Squared 4339.93 3865.57 1.12271
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Rooted Subtracted 32.0372 30.9782 1.059
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Squared 1 29101.9 35347 6245.1
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured 0 170.5 122 48.5
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Rooted Divided 45.1768 47.1159 1.04292
367 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 1 49.0882 54.2027 1.10419

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/