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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Gene Hugo expected measured description Rank final
Results: HTML CSV LaTeX Showing element 1 to 50 of 3206 in total
Hugo  : no value
expected
measured
description
Rank
final
0.0754368 0.0174991 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 1916 0.231970338
0.0871461 0.0193287 MASPIN PRECURSOR (PROTEASE INHIBITOR 5). [SWISSPROT;Acc:P36952] 2320 0.2217965
0.0875599 0.0194204 SERPIN B11. [SWISSPROT;Acc:Q96P15] 2326 0.221795594
0.0887019 0.0214576 DJ1099D15.1 (PUTATIVE DNAJ PROTEIN). [SPTREMBL;Acc:Q9H4J9] 1540 0.241906881
0.0900703 0.0199772 CYTOPLASMIC ANTIPROTEINASE 2 (CAP2) (CAP-2) (PROTEASE INHIBITOR 8) (SERPIN B8). [SWISSPROT;Acc:P50452] 2324 0.221795642
0.0901539 0.02137 1731 0.237039108
0.0991465 0.0259096 "MYOSIN LIGHT CHAIN 1, EMBRYONIC MUSCLE/ATRIAL ISOFORM (PRO1957). [SWISSPROT;Acc:P12829]" 820 0.261326421
0.100647 0.0202703 DJ570F3.6 (NOVEL PROTEIN SIMILAR TO LYSOPHOSPHOLIPASE II (LYPLA2)). [SPTREMBL;Acc:Q9UGE0] 2773 0.201399942
0.101375 0.0217565 2541 0.214614057
0.104626 0.0286746 ENIGMA PROTEIN; LIM DOMAIN PROTEIN. [RefSeq;Acc:NM_005451] 504 0.274067631
0.105517 0.024834 17 BETA-HYDROXYSTEROID DEHYDROGENASE. [SPTREMBL;Acc:Q13034] 1782 0.23535544
0.106766 0.0285187 SECRETED MODULAR CALCIUM-BINDING PROTEIN 1. [RefSeq;Acc:NM_022137] 659 0.267114063
0.110551 0.0281805 HUNTINGTIN INTERACTING PROTEIN E; HUNTINGTIN INTERACTOR PROTEIN E. [RefSeq;Acc:NM_007076] 1003 0.254909499
0.110947 0.0334849 "FATTY ACID-BINDING PROTEIN, EPIDERMAL (E-FABP) (PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG) (PA-FABP). [SWISSPROT;Acc:Q01469]" 287 0.301809873
0.1121 0.0296502 BA508N22.1 (HSPC025) (FRAGMENT). [SPTREMBL;Acc:Q9HCW5] 745 0.26449777
0.112137 0.0240826 KERATIN ASSOCIATED PROTEIN 2-4; KERATIN ASSOCIATED PROTEIN 2.4. [RefSeq;Acc:NM_033184] 2533 0.214760516
0.114163 0.0298281 PUTATIVE ANKYRIN-REPEAT CONTAINING PROTEIN. [RefSeq;Acc:NM_025185] 827 0.261276421
0.11537 0.0275762 1647 0.23902401
0.116288 0.0249741 KERATIN ASSOCIATED PROTEIN 1.5. [RefSeq;Acc:NM_031957] 2532 0.214760766
0.116854 0.0250957 "KERATIN, ULTRA HIGH-SULFUR MATRIX PROTEIN A (UHS KERATIN A) (UHS KERA). [SWISSPROT;Acc:P26371]" 2530 0.214761155
0.117581 0.0274494 1854 0.233450983
0.117689 0.0258973 THIAMIN PYROPHOSPHOKINASE 1; MOUSE THIAMIN PYROPHOSPHOKINASE HOMOLOG; THIAMINE PYROPHOSPHOKINASE. [RefSeq;Acc:NM_022445] 2375 0.220048603
0.117865 0.0275157 PRESENILIN-LIKE PROTEIN 2 (EC 3.4.99.-) (SPPL2A PROTEIN). [SWISSPROT;Acc:Q8TCT8] 1855 0.233450982
0.118668 0.0310375 BRAIN PROTEIN 16. [RefSeq;Acc:NM_016458] 811 0.261549028
0.118824 0.027225 PREFOLDIN SUBUNIT 6 (PROTEIN KE2). [SWISSPROT;Acc:O15212] 2077 0.22912038
0.120086 0.0255653 DC11 PROTEIN. [RefSeq;Acc:NM_020186] 2590 0.212891594
HEPATITIS C VIRUS CORE-BINDING PROTEIN 6; CERVICAL CANCER ONCOGENE 3. [RefSeq;Acc:NM_023934] 2592
0.120439 0.0258656 KERATIN ASSOCIATED PROTEIN 1-3; KERATIN ASSOCIATED PROTEIN 1.3. [RefSeq;Acc:NM_030966] 2531 0.214760999
0.120774 0.02527 NEURAL CELL ADHESION MOLECULE L1 PRECURSOR (N-CAM L1) (CD171 ANTIGEN). [SWISSPROT;Acc:P32004] 2666 0.209233775
0.121383 0.0260682 KERATIN ASSOCIATED PROTEIN 4.3 (FRAGMENT). [SPTREMBL;Acc:Q9BYR4] 2534 0.214759892
0.121579 0.0321572 LIPOPOLYSACCHARIDE-RESPONSIVE AND BEIGE-LIKE ANCHOR PROTEIN (CDC4-LIKE PROTEIN) (BEIGE-LIKE PROTEIN). [SWISSPROT;Acc:P50851] 752 0.264496336
0.122543 0.0413389 FILAMIN A (ALPHA-FILAMIN) (FILAMIN 1) (ENDOTHELIAL ACTIN-BINDING PROTEIN) (ABP-280) (NONMUSCLE FILAMIN). [SWISSPROT;Acc:P21333] 178 0.337341994
0.122748 0.034272 373 0.279206179
0.124441 0.0511645 "DJ681N20.2 (NOVEL PROTEIN SIMILAR TO FERRITIN, LIGHT POLYPEPTIDE (FTL)). [SPTREMBL;Acc:Q9BYW6]" 58 0.411154684
0.125634 0.0344618 492 0.274303135
0.126946 0.0308447 1481 0.242974966
0.128294 0.029603 2002 0.230743449
0.128445 0.0322794 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] 1099 0.251309121
0.129724 0.031639 NUCLEAR RECEPTOR CO-REPRESSOR/HDAC3 COMPLEX SUBUNIT TBLR1 (TBL1- RELATED PROTEIN 1). [SWISSPROT;Acc:Q9BZK7] 1423 0.24389473
0.130722 0.0280741 KERATIN ASSOCIATED PROTEIN 4-10; KERATIN ASSOCIATED PROTEIN 4.10. [RefSeq;Acc:NM_033060] 2529 0.214761861
0.130845 0.0373117 GA BINDING PROTEIN BETA-2 CHAIN (GABP-BETA-2 SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-47) (GAPBP-2) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT GAMMA). [SWISSPROT;Acc:Q06545] 333 0.28515954
0.136094 0.0368814 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN 2 (FOVEA-ASSOCIATED SH3 DOMAIN BINDING PROTEIN). [SWISSPROT;Acc:Q9UJC5] 554 0.270999456
0.13696 0.031325 2088 0.228716414
0.138898 0.0320499 POLY (ADP-RIBOSE) GLYCOHYDROLASE. [RefSeq;Acc:NM_003631] 2001 0.230744143
0.139602 0.0367538 "SIRTUIN 7; SIR2-RELATED PROTEIN TYPE 7; SIRTUIN TYPE 7; SIRTUIN (SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG) 7; SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG 7; SIRTUIN SILENT MATING TYPE INFORMATION REGULATION" 773 0.263275598
0.141189 0.030828500000000002 2413 0.218349163
0.142049 0.0331615 1853 0.233451133
PRESENILIN-LIKE PROTEIN 1 (EC 3.4.99.-) (SPPL2B PROTEIN). [SWISSPROT;Acc:Q8TCT7] 1852
0.142328 0.0429558 "BETA-CAROTENE DIOXYGENASE 2; PUTATIVE B,B-CAROTENE-9',10'-DIOXYGENASE. [RefSeq;Acc:NM_031938]" 294 0.301808499
0.144194 0.0378601 784 0.26256363

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/