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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2908 to 2957 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
364 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 0 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
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 17957.2 22234.1 1.23817
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Rooted 0 53.8642 56.248 1.04426
365 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Ranked 1 242.744 266.07 1.09609
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Squared 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
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Measured 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
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Ranked 0 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
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Squared 62783.5 50784.1 1.23628
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured 5189 6088.47 1.17334
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Ranked 0 8614.89 9017.27 1.04671
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 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
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Rooted 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
basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Squared 62757.7 50767.8 1.23617
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Measured 4024.4 4719.35 1.17268
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 0 2039.47 2164.92 1.06151
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Ranked 13801.7 13185.9 1.0467
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Squared 72128.6 64272.5 1.12223
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Ranked 1 234.146 256.627 1.09601
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Rooted 0 45.1768 47.1159 1.04292
368 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Ranked 16679.2 15940.6 1.04633
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] Rooted 17.8274 17.1002 1.04253
dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Squared 1 51805.2 41916.4 1.23592
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Measured 0 5946.96 5606.29 1.06077
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Rooted 1 49.5225 54.6817 1.10418
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Measured 5082.66 5959.99 1.17261
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Squared 0 346.699 309.317 1.12085
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Ranked 1 242.66 265.715 1.09501
369 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 0 18849.7 19704.7 1.04536
60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 1 242.159 265.104 1.09475
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Measured 3583.56 4194.95 1.17061
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 0 1048.65 988.882 1.06044
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Squared 1 45960.8 56749.6 1.23474
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Rooted 49.7435 45.0586 1.10397
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Squared 0 346.699 309.317 1.12085
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] Rooted 17.8274 17.1002 1.04253
370 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 30.7424 32.0298 1.04188
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Measured 1049.21 989.438 1.06041
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] 1 4108.15 4808.93 1.17058
methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Rooted 49.7435 45.0586 1.10397
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Ranked 242.159 265.104 1.09475

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/