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

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/