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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description Rank Gene Hugo final measured expected
Results: HTML CSV LaTeX Showing element 551 to 600 of 3206 in total
description
Rank
Hugo
final
measured
expected
"BREAST CARCINOMA AMPLIFIED SEQUENCE 2; SPLICEOSOME ASSOCIATED PROTEIN, AMPLIFIED IN BREAST CANCER. [RefSeq;Acc:NM_005872]" 519 BCAS2 0.272249901 0.0379775 0.139495
"C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC (C1-THF SYNTHASE) [INCLUDES: METHYLENETETRAHYDROFOLATE DEHYDROGENASE (EC 1.5.1.5); METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE (EC 3.5.4.9); FORMYLTETRAHYDROFOLATE SYNTHETASE (EC 6.3.4.3)]. [SWISSPROT;Acc:P115" 1784 MTHFD1 0.23524777 0.156153 0.663781
"C316G12.2 (NOVEL PROTEIN SIMILAR TO PREDICTED YEAST, WORM AND ARCHAE- BACTERIAL PROTEINS) (SIMILAR TO UND313) (S. CERVISIAE) (HYPOTHETICAL PROTEIN). [SPTREMBL;Acc:Q9UJK0]" 364 C16orf42 0.280097208 0.131623 0.469919
"CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR1 (SOLUTE CARRIER FAMILY 25, MEMBER 12). [SWISSPROT;Acc:O75746]" 2593 SLC25A12 0.212890762 0.0255652 0.120086
"CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR2 (SOLUTE CARRIER FAMILY 25, MEMBER 13) (CITRIN). [SWISSPROT;Acc:Q9UJS0]" 2589 SLC25A13 0.212891813 0.0223249 0.104865
"CALCIUM-DEPENDENT PROTEASE, SMALL SUBUNIT (CALPAIN REGULATORY SUBUNIT) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP). [SWISSPROT;Acc:P04632]" 118 CAPNS1 0.361134394 0.133134 0.368655
"CALCIUM-TRANSPORTING ATPASE TYPE 2C, MEMBER 1 (EC 3.6.3.8) (ATPASE 2C1) (ATP-DEPENDENT CA(2+) PUMP PMR1) (HUSSY-28). [SWISSPROT;Acc:P98194]" 1455 ATP2C1 0.243146454 0.0944765 0.388558
"CALPAIN 1, LARGE [CATALYTIC] SUBUNIT (EC 3.4.22.17) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP) (MU-TYPE) (MUCANP) (MICROMOLAR-CALPAIN). [SWISSPROT;Acc:P07384]" 301 CAPN1 0.299868312 0.205623 0.685711
"CALPAIN 2, LARGE [CATALYTIC] SUBUNIT PRECURSOR (EC 3.4.22.17) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP) (M-TYPE) (M-CALPAIN) (MILLIMOLAR-CALPAIN) (CALPAIN LARGE POLYPEPTIDE L2). [SWISSPROT;Acc:P17655]" 300 CAPN2 0.299872416 0.201663 0.672496
"CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-ALPHA). [SWISSPROT;Acc:P17612]" 1628 PRKACA 0.239365467 0.210706 0.880269
"CAMP-DEPENDENT PROTEIN KINASE, BETA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-BETA). [SWISSPROT;Acc:P22694]" 1627 PRKACB
"CAMP-DEPENDENT PROTEIN KINASE, GAMMA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-GAMMA). [SWISSPROT;Acc:P22612]" 1626 PRKACG 0.239365758 0.190544 0.796037
"CASEIN KINASE I, ALPHA ISOFORM (EC 2.7.1.-) (CKI-ALPHA) (CK1). [SWISSPROT;Acc:P48729]" 2038 CSNK1A1 0.230172804 0.0909346 0.395071
"CASEIN KINASE I, DELTA ISOFORM (EC 2.7.1.-) (CKI-DELTA) (CKID). [SWISSPROT;Acc:P48730]" 2239 CSNK1D 0.223940006 0.292497 1.30614
"CASEIN KINASE I, EPSILON ISOFORM (EC 2.7.1.-) (CKI-EPSILON) (CKIE). [SWISSPROT;Acc:P49674]" 2233 no value 0.224201149 0.273568 1.22019
"CASEIN KINASE II, ALPHA CHAIN (CK II) (EC 2.7.1.37). [SWISSPROT;Acc:P19138]" 1094 CSNK2A1P 0.251512583 0.23379 0.929536
"CASEIN KINASE II, ALPHA' CHAIN (CK II) (EC 2.7.1.37). [SWISSPROT;Acc:P19784]" 1093 CSNK2A2
"CATENIN (CADHERIN-ASSOCIATED PROTEIN), ALPHA-LIKE 1; ALPHA-CATULIN. [RefSeq;Acc:NM_003798]" 2875 CTNNAL1 0.188434111 0.0374428 0.198705
"CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 4; NOT4 (NEGATIVE REGULATOR OF TRANSCRIPTION 4, YEAST) HOMOLOG; CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT. [RefSeq;Acc:NM_013316]" 430 CNOT4 0.277366829 0.176985 0.63809
"CDC5-LIKE; CDC5 (CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG)-LIKE; CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG-LIKE; CDC5-RELATED PROTEIN. [RefSeq;Acc:NM_001253]" 520 CDC5L 0.272249836 0.333016 1.2232
"CHANNEL ASSOCIATED PROTEIN OF SYNAPSE-110 (CHAPSYN-110) (DISCS, LARGE HOMOLOG 2). [SWISSPROT;Acc:Q15700]" 866 DLG2 0.260273394 0.141754 0.544635
"CHAPERONE-ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL PRECURSOR (CHAPERONE-ABC1-LIKE). [SWISSPROT;Acc:Q8NI60]" 1650 CABC1 0.238973393 0.0340138 0.142333
"CHROMODOMAIN PROTEIN, Y CHROMOSOME-LIKE ISOFORM A; CDY-LIKE, AUTOSOMAL; TESTIS-SPECIFIC CHROMODOMAIN Y-LIKE PROTEIN. [RefSeq;Acc:NM_004824]" 2483 CDYL 0.216308095 0.663776 3.06866
"CIRHIN; TESTIS EXPRESSED GENE 292; CIRRHOSIS, AUTOSOMAL RECESSIVE 1A. [RefSeq;Acc:NM_032830]" 1502 CIRH1A 0.242717998 0.588096 2.42296
"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]" 2741 CPSF4 0.204821697 0.364089 1.77759
"CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 5, 25 KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR IM (25KD); PRE-MRNA CLEAVAGE FACTOR IM, 25KD SUBUNIT. [RefSeq;Acc:NM_007006]" 359 NUDT21 0.281402552 0.288916 1.0267
"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]" 471 CPSF6 0.274547913 1.05805 3.85379
"CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 100 KDA SUBUNIT (CPSF 100 KDA SUBUNIT) (FRAGMENT). [SWISSPROT;Acc:Q9P2I0]" 2740 CPSF2 0.205155373 0.366149 1.78474
"CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 160 KDA SUBUNIT (CPSF 160 KDA SUBUNIT). [SWISSPROT;Acc:Q10570]" 2749 CPSF1 0.204203283 0.334146 1.63634
"CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 73 KDA SUBUNIT (CPSF 73 KDA SUBUNIT). [SWISSPROT;Acc:Q9UKF6]" 2704 CPSF3 0.207511104 0.412088 1.98586
"CLEAVAGE STIMULATION FACTOR SUBUNIT 3; CLEAVAGE STIMULATION FACTOR, 3' PRE-RNA, SUBUNIT 3, 77KD. [RefSeq;Acc:NM_001326]" 2618 CSTF3 0.210596477 0.412171 1.95716
"CLEAVAGE STIMULATION FACTOR, 64 KDA SUBUNIT (CSTF 64 KDA SUBUNIT) (CF-1 64 KDA SUBUNIT). [SWISSPROT;Acc:P33240]" 2128 CSTF2 0.228080738 0.386793 1.69586
"COFILIN, MUSCLE ISOFORM (COFILIN 2). [SWISSPROT;Acc:Q9Y281]" 372 CFL2 0.279207723 0.0460179 0.164816
"COFILIN, NON-MUSCLE ISOFORM (18 KDA PHOSPHOPROTEIN) (P18). [SWISSPROT;Acc:P23528]" 370 CFL1
"COMPLEMENT COMPONENT 1, Q SUBCOMPONENT BINDING PROTEIN, MITOCHONDRIAL PRECURSOR (GLYCOPROTEIN GC1QBP) (GC1Q-R PROTEIN) (HYALURONAN-BINDING PROTEIN 1) (P32) (P33). [SWISSPROT;Acc:Q07021]" 2051 C1QBP 0.229945442 0.532733 2.31678
"COP9 COMPLEX SUBUNIT 4; LIKELY ORTHOLOG OF MOUSE COP9 (CONSTITUTIVE PHOTOMORPHOGENIC), SUBUNIT 4 (ARABIDOPSIS); COP9 (CONSTITUTIVE PHOTOMORPHOGENIC, ARABIDOPSIS, HOMOLOG) SUBUNIT 4. [RefSeq;Acc:NM_016129]" 1195 COPS4 0.248524151 0.161995 0.651828
"COP9 SUBUNIT 6 (MOV34 HOMOLOG, 34 KD). [RefSeq;Acc:NM_006833]" 1176 COPS6 0.249396272 0.0403386 0.161745
"COPROPORPHYRINOGEN III OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.3) (COPROPORPHYRINOGENASE) (COPROGEN OXIDASE) (COX). [SWISSPROT;Acc:P36551]" 1467 CPOX 0.243016695 0.0753291 0.309975
"CREATINE KINASE, B CHAIN (EC 2.7.3.2) (B-CK). [SWISSPROT;Acc:P12277]" 1870 CKB 0.232840254 0.235164 1.00998
"CREATINE KINASE, M CHAIN (EC 2.7.3.2) (M-CK). [SWISSPROT;Acc:P06732]" 1894 CKM 0.232621726 0.219925 0.945419
"CREATINE KINASE, SARCOMERIC MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (S- MTCK) (MIB-CK) (BASIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P17540]" 1883 CKMT2 0.232752435 0.197547 0.848743
"CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (U- MTCK) (MIA-CK) (ACIDIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P12532]" 1882 no value 0.232757243 0.199469 0.856983
"CUG TRIPLET REPEAT, RNA BINDING PROTEIN 2; ELAV-TYPE RNA-BINDING PROTEIN; CUG TRIPLET REPEAT,RNA-BINDING PROTEIN 2; CUG TRIPLET REPEAT, RNA-BINDING PROTEIN 2; NEUROBLASTOMA APOPTOSIS-RELATED RNA-BINDING PROTEIN. [RefSeq;Acc:NM_006561]" 547 CUGBP2 0.271003728 0.24526 0.905006
"CYLINDROMATOSIS (TURBAN TUMOR SYNDROME); CYLINDROMATOSIS 1, TURBAN TUMOR SYNDROME. [RefSeq;Acc:NM_015247]" 1256 CYLD 0.247334342 0.0366317 0.148106
"CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX11, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q9Y6N1]" 2546 COX11 0.214613263 0.124724 0.581157
"CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 1, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-1) (CYTOCHROME C OXIDASE POLYPEPTIDE IV). [SWISSPROT;Acc:P13073]" 2101 COX4I1 0.228353307 0.0360136 0.15771
"CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 2, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-2). [SWISSPROT;Acc:Q96KJ9]" 2099 COX4I2
"CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL PRECURSOR (CYTOCHROME C-1). [SWISSPROT;Acc:P08574]" 1621 CYC1 0.239596694 0.150184 0.62682
"CYTOCHROME OXIDASE BIOGENESIS PROTEIN OXA1, MITOCHONDRIAL PRECURSOR (OXA1-LIKE PROTEIN) (OXA1HS). [SWISSPROT;Acc:Q15070]" 1127 OXA1L 0.250657759 0.168913 0.673879
"DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 39 ISOFORM 1; NUCLEAR RNA HELICASE, DECD VARIANT OF DEAD BOX FAMILY. [RefSeq;Acc:NM_005804]" 1758 DDX39 0.236715713 0.0299559 0.126548

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/