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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Hugo measured Gene final Rank description expected
Results: HTML CSV LaTeX Showing element 1 to 50 of 3206 in total
Hugo  : no value
measured
final
Rank
description
expected
0.000173011 0.000219976 3206 0.7865
0.000178236 0.000219977 3204 ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [RefSeq;Acc:NM_015915] 0.81025
0.0174991 0.231970338 1916 BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETHASE 2 (PAPS SYNTHETHASE 2) (PAPSS 2) (SULFURYLASE KINASE 2) (SK2) (SK 2) [INCLUDES: SULFATE ADENYLYLTRANSFERASE (EC 2.7.7.4) (SULFATE ADENYLATE TRANSFERASE) (SAT) (ATP-SULFURYLASE); ADENYLYLSULFAT 0.0754368
0.0193287 0.2217965 2320 MASPIN PRECURSOR (PROTEASE INHIBITOR 5). [SWISSPROT;Acc:P36952] 0.0871461
0.0194204 0.221795594 2326 SERPIN B11. [SWISSPROT;Acc:Q96P15] 0.0875599
0.0199772 0.221795642 2324 CYTOPLASMIC ANTIPROTEINASE 2 (CAP2) (CAP-2) (PROTEASE INHIBITOR 8) (SERPIN B8). [SWISSPROT;Acc:P50452] 0.0900703
0.0202703 0.201399942 2773 DJ570F3.6 (NOVEL PROTEIN SIMILAR TO LYSOPHOSPHOLIPASE II (LYPLA2)). [SPTREMBL;Acc:Q9UGE0] 0.100647
0.02137 0.237039108 1731 0.0901539
0.0214576 0.241906881 1540 DJ1099D15.1 (PUTATIVE DNAJ PROTEIN). [SPTREMBL;Acc:Q9H4J9] 0.0887019
0.0217565 0.214614057 2541 0.101375
0.0240826 0.214760516 2533 KERATIN ASSOCIATED PROTEIN 2-4; KERATIN ASSOCIATED PROTEIN 2.4. [RefSeq;Acc:NM_033184] 0.112137
0.024834 0.23535544 1782 17 BETA-HYDROXYSTEROID DEHYDROGENASE. [SPTREMBL;Acc:Q13034] 0.105517
0.0249741 0.214760766 2532 KERATIN ASSOCIATED PROTEIN 1.5. [RefSeq;Acc:NM_031957] 0.116288
0.0250043 0.119322081 3024 SYNBINDIN (TRS23 HOMOLOG) (HEMATOPOIETIC STEM/PROGENITOR CELL PROTEIN 172) (HSPC172) (PTD009) (CGI-104). [SWISSPROT;Acc:Q9Y296] 0.209553
0.0250957 0.214761155 2530 "KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN A (UHS KERATIN A) (UHS KERA). [SWISSPROT;Acc:P26371]" 0.116854
0.02527 0.209233775 2666 NEURAL CELL ADHESION MOLECULE L1 PRECURSOR (N-CAM L1) (CD171 ANTIGEN). [SWISSPROT;Acc:P32004] 0.120774
0.0255653 0.212891594 2590 DC11 PROTEIN. [RefSeq;Acc:NM_020186] 0.120086
2592 HEPATITIS C VIRUS CORE-BINDING PROTEIN 6; CERVICAL CANCER ONCOGENE 3. [RefSeq;Acc:NM_023934]
0.0258656 0.214760999 2531 KERATIN ASSOCIATED PROTEIN 1-3; KERATIN ASSOCIATED PROTEIN 1.3. [RefSeq;Acc:NM_030966] 0.120439
0.0258973 0.220048603 2375 THIAMIN PYROPHOSPHOKINASE 1; MOUSE THIAMIN PYROPHOSPHOKINASE HOMOLOG; THIAMINE PYROPHOSPHOKINASE. [RefSeq;Acc:NM_022445] 0.117689
0.0259096 0.261326421 820 "MYOSIN LIGHT CHAIN 1, EMBRYONIC MUSCLE/ATRIAL ISOFORM (PRO1957). [SWISSPROT;Acc:P12829]" 0.0991465
0.0260682 0.214759892 2534 KERATIN ASSOCIATED PROTEIN 4.3 (FRAGMENT). [SPTREMBL;Acc:Q9BYR4] 0.121383
0.027225 0.22912038 2077 PREFOLDIN SUBUNIT 6 (PROTEIN KE2). [SWISSPROT;Acc:O15212] 0.118824
0.0274494 0.233450983 1854 0.117581
0.0275157 0.233450982 1855 PRESENILIN-LIKE PROTEIN 2 (EC 3.4.99.-) (SPPL2A PROTEIN). [SWISSPROT;Acc:Q8TCT8] 0.117865
0.0275762 0.23902401 1647 0.11537
0.0280741 0.214761861 2529 KERATIN ASSOCIATED PROTEIN 4-10; KERATIN ASSOCIATED PROTEIN 4.10. [RefSeq;Acc:NM_033060] 0.130722
0.0281805 0.254909499 1003 HUNTINGTIN INTERACTING PROTEIN E; HUNTINGTIN INTERACTOR PROTEIN E. [RefSeq;Acc:NM_007076] 0.110551
0.0285187 0.267114063 659 SECRETED MODULAR CALCIUM-BINDING PROTEIN 1. [RefSeq;Acc:NM_022137] 0.106766
0.0286746 0.274067631 504 ENIGMA PROTEIN; LIM DOMAIN PROTEIN. [RefSeq;Acc:NM_005451] 0.104626
0.028817 0.037315105 3187 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14C; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-81; PKC-POTENTIATED PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_030949]" 0.772261
0.029603 0.230743449 2002 0.128294
0.0296502 0.26449777 745 BA508N22.1 (HSPC025) (FRAGMENT). [SPTREMBL;Acc:Q9HCW5] 0.1121
0.0298281 0.261276421 827 PUTATIVE ANKYRIN-REPEAT CONTAINING PROTEIN. [RefSeq;Acc:NM_025185] 0.114163
0.030828500000000002 0.218349163 2413 0.141189
0.0308447 0.242974966 1481 0.126946
0.0308655 0.139559332 2978 HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). [SWISSPROT;Acc:P09630] 0.221164
0.0310375 0.261549028 811 BRAIN PROTEIN 16. [RefSeq;Acc:NM_016458] 0.118668
0.0310799 0.13955887 2983 HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). [SWISSPROT;Acc:Q00056] 0.222701
0.0311872 0.139559402 2976 HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). [SWISSPROT;Acc:P09017] 0.223469
0.0312313 0.188940513 2866 HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2. [RefSeq;Acc:NM_032631] 0.165297
0.0312821 0.10668074 3049 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. [SWISSPROT;Acc:Q9Y3K8] 0.293231
0.031325 0.228716414 2088 0.13696
0.0313747 0.206548387 2723 0.1519
0.0314375 0.21476196 2528 KERATIN ASSOCIATED PROTEIN 4-2; KERATIN ASSOCIATED PROTEIN 4.2. [RefSeq;Acc:NM_033062] 0.146383
0.031639 0.24389473 1423 NUCLEAR RECEPTOR CO-REPRESSOR/HDAC3 COMPLEX SUBUNIT TBLR1 (TBL1- RELATED PROTEIN 1). [SWISSPROT;Acc:Q9BZK7] 0.129724
0.0320499 0.230744143 2001 POLY (ADP-RIBOSE) GLYCOHYDROLASE. [RefSeq;Acc:NM_003631] 0.138898
0.0321572 0.264496336 752 LIPOPOLYSACCHARIDE-RESPONSIVE AND BEIGE-LIKE ANCHOR PROTEIN (CDC4-LIKE PROTEIN) (BEIGE-LIKE PROTEIN). [SWISSPROT;Acc:P50851] 0.121579
0.0322794 0.251309121 1099 PHOSPHOGLYCERATE MUTASE 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (PHOSPHOGLYCERATE MUTASE ISOZYME B) (PGAM-B) (BPG-DEPENDENT PGAM 1). [SWISSPROT;Acc:P18669] 0.128445
0.0331615 0.233451133 1852 PRESENILIN-LIKE PROTEIN 1 (EC 3.4.99.-) (SPPL2B PROTEIN). [SWISSPROT;Acc:Q8TCT7] 0.142049

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/