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.


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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3058 to 3107 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
383 no value hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Measured Divided 4533.74 5279.4 1.16447
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Rooted Subtracted 46.1476 52.5742 6.4266
MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Divided 49.8325 45.2077 1.1023
RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Ranked 237.862 217.739 1.09242
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured Subtracted 4247.36 5192.61 945.25
TRUB1 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Ranked 236.245 255.113 18.868
TULP1 tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Squared 30286.5 36362 6075.5
384 no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Rooted Divided 50.7723 46.0607 1.10229
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Measured 4533.74 5279.4 1.16447
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Ranked Subtracted 227.575 208.756 18.819
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Rooted 56.185 62.6036 6.4186
E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Ranked Divided 266.421 244.236 1.09083
HARS2 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Measured Subtracted 8061.05 9002.33 941.28
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Squared Divided 15043.7 18560.1 1.23375
VPS29 vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Subtracted 30286.5 36362 6075.5
385 ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Rooted 87.4586 81.0798 6.3788
BCCIP brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Divided 50.7723 46.0607 1.10229
E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Ranked 266.421 244.236 1.09083
HARS histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Measured Subtracted 8056.09 8996.46 940.37
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Squared Divided 15043.7 18560.1 1.23375
NUMBL numb-like protein (numb-r). [swissprot;acc:q9y6r0] Subtracted 30286.5 36362 6075.5
PSIP1 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Measured Divided 4533.74 5279.4 1.16447
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Ranked Subtracted 227.575 208.756 18.819
386 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Measured 1833.01 892.67 940.34
scratch; scratch 1. [refseq;acc:nm_031309] Squared Divided 40388.9 49827.5 1.23369
CLEC3B tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Rooted Subtracted 86.1101 92.4812 6.3711
EIF1B protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Divided 50.0513 45.4124 1.10215
RPL8 60s ribosomal protein l8. [swissprot;acc:p25120] Measured 4533.74 5279.4 1.16447
RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Ranked 242.238 264.11 1.09029
RPS9 40s ribosomal protein s9. [swissprot;acc:p46781] Subtracted 238.986 257.784 18.798
TULP3 tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Squared 30286.5 36362 6075.5
387 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Ranked Divided 242.238 264.11 1.09029
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Rooted 50.3345 45.6718 1.10209
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Subtracted 98.2298 91.8648 6.365
ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Ranked 56.6768 75.3531 18.6763
EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Squared Divided 15053 18568 1.23351
GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Measured Subtracted 1833.01 892.67 940.34
HDGF hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Divided 4533.74 5279.4 1.16447
VPS35 vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Squared Subtracted 30286.5 36362 6075.5
388 no value dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Divided 40315.7 49716.4 1.23318
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Ranked 227.575 208.756 1.09015
ARID1A swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Measured Subtracted 6252.58 7192.88 940.3
HDGFL1 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Divided 4533.74 5279.4 1.16447
MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Ranked Subtracted 56.7244 75.3948 18.6704
PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Rooted 58.6096 64.9655 6.3559
PRKCZ protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Squared 30286.5 36362 6075.5
SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Rooted Divided 50.3345 45.6718 1.10209
389 ADSS adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared Subtracted 26819.1 32855.4 6036.3
DDX6 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Measured Divided 4533.74 5279.4 1.16447
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Ranked Subtracted 56.7252 75.3954 18.6702

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/