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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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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3964 to 4013 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1982 SLC27A6 very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] Subtracted 191.41 193.389 1.979
1983 PDLIM5 lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] Divided 219.25 217.175 1.00955
SLC27A5 solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] Subtracted 191.408 193.387 1.979
1984 DIP2B similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] 191.415 193.394
EP400 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Divided 219.26 217.193 1.00952
1985 LIN7C lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] Subtracted 225.015 223.041 1.974
MRPL24 mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] Divided 219.26 217.193 1.00952
1986 RHD blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Subtracted 196.964 198.935 1.971
YAP1 65 kda yes-associated protein (yap65). [swissprot;acc:p46937] Divided 219.26 217.193 1.00952
1987 no value blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Subtracted 196.964 198.935 1.971
LIN7A lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] Divided 225.022 222.9 1.00952
1988 no value blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Subtracted 196.965 198.936 1.971
CCDC130 9 kda protein. [swissprot;acc:p13994] Divided 219.26 217.193 1.00952
1989 COL4A3 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] 219.261 217.195 1.00951
PPP1R12B protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Subtracted 217.662 215.693 1.969
1990 no value collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Divided 219.26 217.194 1.00951
PPP1R12A protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Subtracted 217.676 215.709 1.967
1991 TOP3A dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 217.941 215.979 1.962
WWTR1 transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] Divided 219.26 217.194 1.00951
1992 CTRL proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] Subtracted 216.201 214.245 1.956
LDB3 zasp protein (fragment). [sptrembl;acc:q9y4z3] Divided 219.267 217.207 1.00948
1993 CKMT2 creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] Subtracted 198.3 196.347 1.953
HIP1R huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Divided 189.052 190.835 1.00943
1994 no value creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Subtracted 198.293 196.341 1.952
COL4A3BP goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Divided 189.011 190.787 1.0094
1995 HIP1 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 188.961 190.73 1.00936
PPIH peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] Subtracted 198.258 196.319 1.939
1996 PRPF18 prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675]
SLC5A5 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Divided 204.682 202.784 1.00936
1997 C21orf55 j domain protein c21orf55. [swissprot;acc:q9nx36] Subtracted 198.257 196.319 1.938
PRODH2 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Divided 204.651 202.759 1.00933
1998 C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 200.219 198.37 1.00932
CKB creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277] Subtracted 198.19 196.252 1.938
1999 no value acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] 215.799 213.865 1.934
SLC5A8 solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Divided 204.636 202.748 1.00931
2000 no value 40s ribosomal protein s28. [swissprot;acc:p25112] Subtracted 200.343 198.427 1.916
SLC5A6 sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Divided 204.626 202.739 1.00931
2001 CKM creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Subtracted 198.258 196.346 1.912
LIN7B lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] Divided 225.02 222.948 1.00929
2002 DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Subtracted 208.315 206.41 1.905
SNRPB2 u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Divided 214.775 216.769 1.00928
2003 DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 208.315 206.41 1.00923
TTRAP traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] Subtracted 218.466 216.562 1.904
2004 ERBB4 receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] Divided 225.019 222.969 1.00919
PCNA proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Subtracted 229.102 231.001 1.899
2005 EGFR epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] Divided 225.019 222.971 1.00919
SLC5A5 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Subtracted 204.682 202.784 1.898
2006 ERBB2 receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] Divided 225.019 222.971 1.00919
LMNB1 lamin b1. [swissprot;acc:p20700] Subtracted 218.919 220.813 1.894
2007 CENTB5 centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] 220.812 1.893

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/