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 Rank Gene expected description final
Results: HTML CSV LaTeX Showing element 902 to 951 of 3206 in total
Hugo
measured
Rank
expected
description
final
CPEB4 0.164494 3071 1.59398 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 4. [RefSeq;Acc:NM_030627] 0.103197029
CPN1 0.0305978 1112 0.121992 CARBOXYPEPTIDASE N CATALYTIC CHAIN PRECURSOR (EC 3.4.17.3) (ARGININE CARBOXYPEPTIDASE) (KININASE 1) (SERUM CARBOXYPEPTIDASE N) (SCPN) (ANAPHYLATOXIN INACTIVATOR) (PLASMA CARBOXYPEPTIDASE B). [SWISSPROT;Acc:P15169] 0.250818086
CPOX 0.0753291 1467 0.309975 "COPROPORPHYRINOGEN III OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.3) (COPROPORPHYRINOGENASE) (COPROGEN OXIDASE) (COX). [SWISSPROT;Acc:P36551]" 0.243016695
CPSF1 0.334146 2749 1.63634 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 160 KDA SUBUNIT (CPSF 160 KDA SUBUNIT). [SWISSPROT;Acc:Q10570]" 0.204203283
CPSF2 0.366149 2740 1.78474 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 100 KDA SUBUNIT (CPSF 100 KDA SUBUNIT) (FRAGMENT). [SWISSPROT;Acc:Q9P2I0]" 0.205155373
CPSF3 0.412088 2704 1.98586 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 73 KDA SUBUNIT (CPSF 73 KDA SUBUNIT). [SWISSPROT;Acc:Q9UKF6]" 0.207511104
CPSF4 0.364089 2741 1.77759 "CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 4, 30KD SUBUNIT; CLEAVAGE-POLYADENYLATION SPECIFICITY FACTOR, 30KD; NO ARCHES-LIKE (ZEBRAFISH) ZINC FINGER PROTEIN; CLEAVAGE-POLYADENYLATION SPECIFICITY FACTOR. [RefSeq;Acc:NM_006693]" 0.204821697
CPSF6 1.05805 471 3.85379 "CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 6, 68 KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR IM (68KD); CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 6, 68KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR I, 68KD SUBUNIT. [RefSeq;Acc:NM_007007]" 0.274547913
CPXM1 0.0302145 1115 0.120464 POTENTIAL CARBOXYPEPTIDASE X PRECURSOR (EC 3.4.17.-) (METALLOCARBOXYPEPTIDASE CPX-1). [SWISSPROT;Acc:Q96SM3] 0.250817672
CPXM2 1114 POTENTIAL CARBOXYPEPTIDASE-LIKE PROTEIN X2 PRECURSOR. [SWISSPROT;Acc:Q8N436]
CPZ 0.0303816 1111 0.12113 CPZ GENE PRODUCT. [RefSeq;Acc:NM_003652] 0.250818129
CRAT 0.193666 204 0.601521 CARNITINE O-ACETYLTRANSFERASE (EC 2.3.1.7) (CARNITINE ACETYLASE) (CAT). [SWISSPROT;Acc:P43155] 0.321960497
CRBN 0.0586994 2170 0.25856 PROTEIN X 0001. [RefSeq;Acc:NM_016302] 0.227024288
CREB5 0.132014 598 0.490424 CAMP RESPONSE ELEMENT-BINDING PROTEIN CRE-BPA. [RefSeq;Acc:NM_004904] 0.2691834
CREBL1 0.0331688 1336 0.135226 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-6 BETA (ACTIVATING TRANSCRIPTION FACTOR 6 BETA) (ATF6-BETA) (CAMP RESPONSIVE ELEMENT BINDING PROTEIN-LIKE 1) (CAMP RESPONSE ELEMENT BINDING PROTEIN-RELATED PROTEIN) (CREB-RP) (G13 PROTEIN). [SWISSPROT;A 0.245284191
CREG1 0.312681 60 0.760495 CELLULAR REPRESSOR OF E1A-STIMULATED GENES. [RefSeq;Acc:NM_003851] 0.411154577
CREG2 0.237385 62 0.577362 CELLULAR REPRESSOR OF E1A-STIMULATED GENES 2. [RefSeq;Acc:NM_153836] 0.411154527
CRIM1 0.516861 1282 2.10021 CYSTEINE-RICH MOTOR NEURON 1; CYSTEINE-RICH REPEAT-CONTAINING PROTEIN S52 PRECURSOR. [RefSeq;Acc:NM_016441] 0.246099676
CRK 0.142264 34 0.337971 PROTO-ONCOGENE C-CRK (P38) (ADAPTER MOLECULE CRK). [SWISSPROT;Acc:P46108] 0.420935524
CRKL 0.142003 35 0.337351 CRK-LIKE PROTEIN. [SWISSPROT;Acc:P46109] 0.420935465
CRLS1 0.354332 2731 1.72277 0.205675743
CRNKL1 0.802935 379 2.8765 CROOKED NECK-LIKE PROTEIN 1 (CROOKED NECK HOMOLOG) (HCRN) (CGI-201) (MSTP021). [SWISSPROT;Acc:Q9BZJ0] 0.279136103
CROT 0.117061 739 0.442554 PEROXISOMAL CARNITINE OCTANOYLTRANSFERASE (EC 2.3.1.-) (COT). [SWISSPROT;Acc:Q9UKG9] 0.264512353
CRX 0.226785 606 0.843068 CONE-ROD HOMEOBOX PROTEIN. [SWISSPROT;Acc:O43186] 0.268999654
CSDA 0.0613805 2189 0.271164 DNA-BINDING PROTEIN A (COLD SHOCK DOMAIN PROTEIN A) (SINGLE-STRAND DNA BINDING PROTEIN NF-GMB). [SWISSPROT;Acc:P16989] 0.226359325
CSDE1 0.0368889 1036 0.145611 UNR PROTEIN. [SWISSPROT;Acc:O75534] 0.25333869
CSE1L 0.0342868 1072 0.135906 IMPORTIN-ALPHA RE-EXPORTER (CHROMOSOME SEGREGATION 1-LIKE PROTEIN) (CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN). [SWISSPROT;Acc:P55060] 0.252283196
CSMD1 0.0586244 610 0.21806 DJ947L8.1.6 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4W2] 0.268845272
CSNK1A1 0.0909346 2038 0.395071 "CASEIN KINASE I, ALPHA ISOFORM (EC 2.7.1.-) (CKI-ALPHA) (CK1). [SWISSPROT;Acc:P48729]" 0.230172804
CSNK1A1L 0.0896146 2037 0.389336 CASEIN KINASE I ALPHA S-LIKE. [RefSeq;Acc:NM_145203] 0.23017291
CSNK1D 0.292497 2239 1.30614 "CASEIN KINASE I, DELTA ISOFORM (EC 2.7.1.-) (CKI-DELTA) (CKID). [SWISSPROT;Acc:P48730]" 0.223940006
CSNK2A1P 0.23379 1094 0.929536 "CASEIN KINASE II, ALPHA CHAIN (CK II) (EC 2.7.1.37). [SWISSPROT;Acc:P19138]" 0.251512583
CSNK2A2 1093 "CASEIN KINASE II, ALPHA' CHAIN (CK II) (EC 2.7.1.37). [SWISSPROT;Acc:P19784]"
CSRP1 0.121467 3120 1.37814 CYSTEINE-RICH PROTEIN 1 (CRP1) (CRP). [SWISSPROT;Acc:P21291] 0.08813836
CSRP2 0.110507 3117 1.25295 SMOOTH MUSCLE CELL LIM PROTEIN (CYSTEINE-RICH PROTEIN 2) (CRP2) (LIM-ONLY PROTEIN 5). [SWISSPROT;Acc:Q16527] 0.088197454
CSRP3 0.101174 3116 1.14635 "LIM DOMAIN PROTEIN, CARDIAC (MUSCLE LIM PROTEIN) (CYSTEINE-RICH PROTEIN 3) (CRP3). [SWISSPROT;Acc:P50461]" 0.088257513
CSTF2 0.386793 2128 1.69586 "CLEAVAGE STIMULATION FACTOR, 64 KDA SUBUNIT (CSTF 64 KDA SUBUNIT) (CF-1 64 KDA SUBUNIT). [SWISSPROT;Acc:P33240]" 0.228080738
CSTF2T 0.388695 2075 1.69606 LIKELY ORTHOLOG OF MOUSE VARIANT POLYADENYLATION PROTEIN CSTF-64. [RefSeq;Acc:NM_015235] 0.229175265
CSTF3 0.412171 2618 1.95716 "CLEAVAGE STIMULATION FACTOR SUBUNIT 3; CLEAVAGE STIMULATION FACTOR, 3' PRE-RNA, SUBUNIT 3, 77KD. [RefSeq;Acc:NM_001326]" 0.210596477
CTBP1 0.349374 733 1.32007 C-TERMINAL BINDING PROTEIN 1 (CTBP1). [SWISSPROT;Acc:Q13363] 0.264663238
CTBP2 0.398698 738 1.50657 C-TERMINAL BINDING PROTEIN 2 (CTBP2). [SWISSPROT;Acc:P56545] 0.264639545
CTH 0.0790456 1242 0.319234 CYSTATHIONINE GAMMA-LYASE (EC 4.4.1.1) (GAMMA-CYSTATHIONASE). [SWISSPROT;Acc:P32929] 0.247610217
CTNNAL1 0.0374428 2875 0.198705 "CATENIN (CADHERIN-ASSOCIATED PROTEIN), ALPHA-LIKE 1; ALPHA-CATULIN. [RefSeq;Acc:NM_003798]" 0.188434111
CTNNB1 0.126011 1012 0.495862 BETA-CATENIN (PRO2286). [SWISSPROT;Acc:P35222] 0.25412514
CTPS 0.288835 957 1.12692 CTP SYNTHASE (EC 6.3.4.2) (UTP--AMMONIA LIGASE) (CTP SYNTHETASE). [SWISSPROT;Acc:P17812] 0.256304795
CTPS2 0.226073 959 0.882186 CYTIDINE TRIPHOSPHATE SYNTHASE II; CTP SYNTHETASE TYPE 2; UTP-AMMONIA LIGASE; CTP SYNTHETASE ISOFORM; CYTIDINE 5'-TRIPHOSPHATE SYNTHETASE 2. [RefSeq;Acc:NM_019857] 0.256264552
CTRL 0.0742909 1071 0.294313 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] 0.252421402
CTSB 0.264212 1281 1.07259 CATHEPSIN B PRECURSOR (EC 3.4.22.1) (CATHEPSIN B1) (APP SECRETASE). [SWISSPROT;Acc:P07858] 0.246330844
CTSL1 0.184799 1033 0.729445 CATHEPSIN L PRECURSOR (EC 3.4.22.15) (MAJOR EXCRETED PROTEIN) (MEP). [SWISSPROT;Acc:P07711] 0.253341924
CTSL2 0.163807 1035 0.646587 CATHEPSIN L2 PRECURSOR (EC 3.4.22.43) (CATHEPSIN V) (CATHEPSIN U). [SWISSPROT;Acc:O60911] 0.253341004

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/